Inhibitors of cyclin-dependent kinases

ABSTRACT

The present invention provides novel compounds of Formula (I), (II), or (III), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. Also provided are methods and kits involving the inventive compounds or compositions for treating and/or preventing proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt&#39;s lymphoma, melanoma, multiple myeloma, breast cancer, Ewing&#39;s sarcoma, osteosarcoma, brain cancer, ovarian cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject. Treatment of a subject with a proliferative disease using a compound or composition of the invention may inhibit the aberrant activity of a kinase, such as a cyclin-dependent kinase (CDK) (e.g., CDK7, CDK12, or CDK13), and therefore, induce cellular apoptosis and/or inhibit transcription in the subject.

RELATED APPLICATIONS

This application is a division of and claims priority under 35 U.S.C. §120 to U.S. Patent application U.S. Ser. No. 15/561,729, filed Sep. 26,2017, which is a national stage filing under 35 U.S.C. § 371 ofinternational PCT application, PCT/US2016/024345, filed Mar. 25, 2016,which claims priority under 35 U.S.C. § 119(e) to U.S. provisionalapplication, U.S. Ser. No. 62/139,352, filed Mar. 27, 2015, each ofwhich is incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under grant number 1 R01CA179483-01A1 awarded by the National Institutes of Health. Thegovernment has certain rights in the invention.

BACKGROUND OF THE INVENTION

The members of the cyclin-dependent kinase (CDK) family play criticalregulatory roles in cell proliferation. There are currently twenty knownmammalian CDKs. While CDK7-CDK13 have been linked to transcription, onlyCDK1, 2, 4, and 6 show demonstrable association with the cell cycle.

Unique among the mammalian CDKs, CDK7 has consolidated kinaseactivities, regulating both the cell cycle and transcription. In thecytosol, CDK7 exists as a heterotrimeric complex and is believed tofunction as a CDK1/2-activating kinase (CAK), whereby phosphorylation ofconserved residues in CDK1/2 by CDK7 is required for full catalytic CDKactivity and cell cycle progression (Desai et al., “Effects ofphosphorylation by CAK on cyclin binding by CDC2 and CDK2.” Mol. CellBiol. 15, 345-350 (1995); Kaldis et al., “Analysis of CAK activitiesfrom human cells.” Eur. J. Biochem. 267, 4213-4221 (2000); Larochelle etal., “Requirements for CDK7 in the assembly of CDK1/cyclin B andactivation of CDK2 revealed by chemical genetics in human cells.” Mol.Cell 25, 839-850 (2007)). In the nucleus, CDK7 forms the kinase core ofthe RNA polymerase (RNAP) II general transcription factor complex and ischarged with phosphorylating the C-terminal domain (CTD) of RNAP II, arequisite step in gene transcriptional initiation (Serizawa. et al.,“Association of CDK-activating kinase subunits with transcription factorTFIIH.” Nature 374, 280-282 (1995); Shiekhattar et al., “CDK-activatingkinase complex is a component of human transcription factor TFIIH.”Nature 374, 283-287 (1995); Drapkin et al., “Human cyclin-dependentkinase-activating kinase exists in three distinct complexes.” Proc.Natl. Acad. Sci. U.S.A. 93, 6488-6493 (1996); Liu. et al., “Twocyclin-dependent kinases promote RNA polymerase II transcription andformation of the scaffold complex.” Mol. Cell Biol. 24, 1721-1735(2004); Akhtar et al., “TFIIH kinase places bivalent marks on thecarboxy-terminal domain of RNA polymerase II.” Mol. Cell 34, 387-393(2009); Glover-Cutter et al., “TFIIH-associated CDK7 kinase functions inphosphorylation of C-terminal domain Ser7 residues, promoter-proximalpausing, and termination by RNA polymerase II.” Mol. Cell Biol. 29,5455-5464 (2009)). Together, the two functions of CDK7, i.e., CAK andCTD phosphorylation, support critical facets of cellular proliferation,cell cycling, and transcription.

CDK12 and CDK13 were identified in cDNA screens for cell cycleregulators. Because their cyclin partners were not yet known, they wereinitially named CRKRS and CDC2L5 (Ko et al., J. Cell Sci., 2001, 114,2591-2603; Marques et al., Biochem Biophys Res Commun., 2000, 279(3):832-837), respectively. They were found to be 1490- and 1512-amino acidproteins, respectively, with a conserved central CTD kinase domain anddegenerate RS domains identified in their N- and C-terminal regions(Even et al., J Cell Biochem., 2006, 99(3), 890-904).

Evidence has shown CDK12 and CDK13 play an important role in cancerdevelopment. A comprehensive genomic approach identified CDK12 to be oneof the most frequently somatically mutated genes in high-grade serousovarian cancer, the most fatal form of the disease (Erratum, Nature,2011, 47-((7353), 609-615). Several identified point mutations in thekinase domain point to the critical importance of the kinase activity ofCDK12 for the development/progression of this disease. CDK12 has alsobeen found to contribute to the development of breast cancer. Notably,CDK12 is located on chromosome 17, within the 17q21 locus that containsseveral candidate genes for breast cancer susceptibility (Kauraniemi etal., Cancer Res., 2001, 61(22), 8235-8240), and it is co-amplified withthe tyrosine kinase receptor ERBB2, a protein amplified andoverexpressed in about 20% of breast tumors. Gene fusion between CDK12and ERBB2 was also detected in gastric cancer (Zang et al., Cancer Res.,2011, 71(1), 29-39). CDK12 is also implicated in the modification oftamoxifen sensitivity in estrogen-positive breast cancer via themodulation of the mitogen-activated protein kinase pathway (Iorns etal., Carcinogenesis, 2009, 30(10): 1696-1701).

Due to the important regulatory functions of kinases, such as CDK7,CDK12, and CDK13, in cell cycle control, cell proliferation,differentiation, and apoptosis, it is important to develop modulators ofthe activities of these kinases, including selective modulators, for useas research tools as well as therapeutic agents in the treatment ofdiseases.

SUMMARY OF THE INVENTION

Cyclin dependent kinases (CDKs), e.g., CDK7, CDK12, and CDK13 are keyregulators of the cell cycle. Their successive activation andinactivation drives the cycle forward. The activity of CDKs is regulatedby multiple mechanisms such as positive and negative phosphorylation,binding of regulatory proteins like cyclins, and CDK inhibitors. MostCDKs require the phosphorylation of a threonine residue located in theT-loop to achieve full kinase activity. This threonine residue isconserved in all CDKs that function in cell cycle regulation. The enzymeresponsible for this phosphorylation is therefore termedCDK-activating-kinase or CAK. CAK complexes have been found to becomposed of CDK7, CDK12, CDK13, cyclin H, and MAT1. Besides its CAKfunction, CDK7, CDK12, and CDK13 also play a role in transcription andpossibly in DNA repair. This suggests that the CDK7, CDK12, and CDK13enzyme complexes are involved in multiple functions in the cell, e.g.,cell cycle control, apoptosis, transcription regulation, and DNA repair.

The present invention provides compounds of Formulae (I)-(III), andpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof. The compounds of Formulae (I)-(III),and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof, may inhibit the activity of akinase. The compounds described herein can selectively inhibit specificCDK subtypes, for example, CDK7, CDK12, or CDK13. In certainembodiments, the compounds of Formulae (I)-(III) are selective for CDK7compared to other kinases. In certain embodiments, the compounds ofFormulae (I)-(III) are selective for CDK12 and/or CDK13 compared toother kinases. The present invention also provides methods of using theinventive compounds, and pharmaceutically acceptable salts, solvates,hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, and compositions thereof, tostudy the inhibition of a kinase (e.g., CDK7, CDK12, and/or CDK13) andas therapeutics for the prevention and/or treatment of diseasesassociated with the overexpression and/or aberrant activity of a kinase(e.g., CDK7, CDK12, and/or CDK13). In certain embodiments, the inventivecompounds are used for the prevention and/or treatment of proliferativediseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia,lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer,Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer,colorectal cancer), benign neoplasms, diseases associated withangiogenesis, inflammatory diseases, autoinflammatory diseases, andautoimmune diseases) in a subject.

Since the discovery of selective inhibitors of CDK7, CDK12, and CDK13has been hampered by the high sequence and structural similarities ofthe kinase domain of CDK family members, the development of selectiveinhibitors of the transcriptional cyclin-dependent kinases (tCDKs) willallow dissection of their individual contributions to the regulation oftranscription and evaluation of their therapeutic potential. Withoutwishing to be bound by any particular theory, the inventive compounds'selectivity for CDK7, CDK12, and/or CDK13 may be due to the compounds'ability to covalently modify a specific cysteine residue of thesekinases (e.g., Cys312 of CDK7, Cys1039 of CDK12, Cys1017 of CDK13).

In one aspect, the present invention provides compounds of Formula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein R¹, R², R³, R⁵, Ring A, Ring B, L¹, and L²are as defined herein.

In one aspect, the present invention provides compounds of Formula (II):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein R¹, R², R³, R⁴, Ring A, Ring B, L¹, and L²are as defined herein.

In one aspect, the present invention provides compounds of Formula(III):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein R¹, R², R³, R⁴, Ring A, Ring B, L¹, and L²are as defined herein.

In another aspect, the present disclosure provides pharmaceuticalcompositions including a compound described herein, and optionally apharmaceutically acceptable excipient. In certain embodiments, thepharmaceutical compositions described herein include a therapeuticallyor prophylactically effective amount of a compound described herein. Thepharmaceutical composition may be useful for treating a proliferativedisease in a subject in need thereof, preventing a proliferative diseasein a subject in need thereof, inhibiting the activity of a proteinkinase in a subject, biological sample, tissue, or cell, and/or inducingapoptosis in a cell. In certain embodiments, the proliferative diseaseis an acute inflammatory disease. In certain embodiments, the acuteinflammatory disease is rheumatoid arthritis, Crohn's disease, orfibrosis.

In another aspect, the present invention provides methods for treatingand/or preventing a proliferative disease. Exemplary proliferativediseases which may be treated include cancer, benign neoplasm, diseasesassociated with angiogenesis, inflammatory diseases, autoinflammatorydiseases, and autoimmune diseases. In certain embodiments, the cancer isone or more selected from the group consisting of pancreatic cancer,lung cancer (e.g. small cell lung cancer (SCLC), and non-small cell lungcancer), prostate cancer, breast cancer, ovarian cancer, kidney cancer,liver cancer, Ewing's sarcoma, osteosarcoma, brain cancer,neuroblastoma, and colorectal cancer.

Another aspect of the invention relates to methods of inhibiting theactivity of a kinase (e.g., CDK (e.g., CDK7, CDK12, CDK13)) in abiological sample or subject. In certain embodiments, the methodinvolves the selective inhibition of CDK7. In certain embodiments, themethod involves the selective inhibition of CDK12. In certainembodiments, the method involves the selective inhibition of CDK13.

Also provided by the present invention are methods of inhibitingtranscription of one or more genes in the cell of a biological sample orsubject. The transcription of genes affected by the activity of CDK7 maybe inhibited by a compound of the invention. In certain embodiments,these genes are one or more selected from the group consisting of MYC,RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1, NEUROD1,NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B, PLK2,TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, FOS1. The transcription of genesaffected by the activity of CDK12 may be inhibited by a compound of theinvention. In certain embodiments, these genes are one or more selectedfrom the group consisting of BRCA1, FANC1, ATR, FANCD2, APEX1, NEK9,CHEK1, CHEK2, ATM, RAD51C, RAD51D, ORC3L, MDC1, TERF2, ERCC4, FANCF,PARP9, RUNX1, MYB, TAL1, MCL1, MYC, BCL2, ETS1, EWS-FLI. Thetranscription of genes affected by the activity of CDK13 may beinhibited by a compound of the invention. In certain embodiments, thegene is SNORA38.

The present invention also provides methods of inhibiting cell growth ina biological sample or subject. In still another aspect, the presentinvention provides methods of inducing apoptosis of a cell in abiological sample or subject.

In yet another aspect, the present invention provides compounds ofFormulae (I)-(III), and pharmaceutically acceptable salts, solvates,hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, and compositions thereof,for use in the treatment of a disease (e.g., a proliferative diseasesuch as cancer) in a subject.

Another aspect of the present disclosure relates to kits comprising acontainer with a compound, or pharmaceutical composition thereof, asdescribed herein. The kits described herein may include a single dose ormultiple doses of the compound or pharmaceutical composition. The kitsmay be useful in a method of the disclosure. In certain embodiments, thekit further includes instructions for using the compound orpharmaceutical composition. A kit described herein may also includeinformation (e.g. prescribing information) as required by a regulatoryagency such as the U.S. Food and Drug Administration (FDA).

The present invention provides methods for administering to a subject inneed thereof an effective amount of a compound, or pharmaceuticalcomposition thereof, as described herein. Also described are methods forcontacting a cell with an effective amount of a compound, orpharmaceutical composition thereof, as described herein. In certainembodiments, a method described herein further includes administering tothe subject an additional pharmaceutical agent. In certain embodiments,a method described herein further includes contacting the cell with anadditional pharmaceutical agent. The methods described herein mayfurther include performing radiotherapy, immunotherapy, and/ortransplantation on the subject.

The details of one or more embodiments of the invention are set forthherein. Other features, objects, and advantages of the invention will beapparent from the Detailed Description, the Examples, and the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments of theinvention and together with the description, serve to explain theprinciples of the invention.

FIG. 1 shows inhibition of Jurkat cell viability by compounds E9, E17,and dinaciclib. Specifically, compounds E9 and E17 irreversibly inhibitJurkat cell viability. The antiproliferative effects of compounds E9 andE17 are present with and without washout, while dinaciclib's effects areabolished with washout. Cells were treated with each compound for 4hours and either no washout (no washout) or had compound removed bywashing cells with media (washout). Sixty-eight (68) hours afterwashout, the cells were assayed for antiproliferative effects. Errorbars indicate +/−SD.

FIG. 2 shows binding of compounds E9 and E17 with CDK12 at twoconcentrations. Compounds E9 and E17 were able to block pulldown ofcyclin K at 1 μM and 200 nM. Specifically, Jurkat cells were treatedwith DMSO, compounds E9, E17, and dinaciclib at two concentrations for 4hours. Decreased pulldown of cyclin K with biotin-THZ1 indicated a lossof CDK12 binding. Cyclin H pulldown was not affected, indicating thatCDK7 binding is not affected.

FIG. 3 shows the effect of compounds E9, E17, and Dinaciclib on thedownstream protein targets. Specifically, compounds E9 and E17 show anirreversible effect on Polymerase II Serine 2 phosphorylation and MCL1levels with and without washout. Dinaciclib is only effective when it ispresent in cells, and its effect is abolished by washout.

FIG. 4 shows evaluation of the exemplified compounds in neuroblastoma(NB) cells. The IC50 values are shown in nM.

FIG. 5 shows that Dinaciclib and Compounds E9, E17, and E18 inhibitJurkat T-cell acute lymphoblastic leukemia (T-ALL) cell proliferation.Compounds E9, E17, and E18 irreversibly inhibit T-ALL cell proliferationwhile Dinaciclib acts as a reversible inhibitor. Jurkat cells wereseeded at a density of 25,000 cells/well in 96-well plates. Cells werethen treated with the indicated compounds in a 10-pt dose escalationformat from 1 nM to 10 μM or DMSO control for 72 hours. After 72 hours,the cells were assayed using CellTiter-Glo Luminescent Cell ViabilityAssay (Promega) to determine cell viability by measuring the amount ofATP present in each sample cell population, which is an indicator ofcell metabolic activity. Results were graphed as fraction of the DMSOcontrol at 72 hours. All data points were performed in biologicaltriplicate. Error bars are +/−SD.

FIG. 6 shows the effect of Dinaciclib and compounds E9, E17, and E18 onthe downstream protein targets. Specifically, reversible inhibitorDinaciclib and covalent inhibitors Compounds E9, E17, and E18 are likelyto downregulate mRNA transcripts of TAL1, RUNX1, and MYB in JurkatT-cell acute lymphoblastic leukemia (T-ALL) cells. Jurkat cells wereseeded at a density of 5 million cells/10 mL. Cells were then treatedwith 200 nM or 1 μM of the indicated compounds or with DMSO control for6 hours. Total RNA was extracted from 5 million cells using the RNeasyPlus Mini Kit (Qiagen) with a gDNA eliminator mini column to removegenomic DNA. mRNA was reverse transcribed into cDNA using theSuperScript III First-Strand Synthesis Kit (Life Technologies) using anoligo-dT primer to capture polyadenylated mRNAs. Quantitative PCR (qPCR)using transcript-specific Taqman probes (Applied Biosystems) was used toassess the effect of compound treatment on the expression of theindicated mRNA transcripts. All experiments shown were performed inbiological triplicate. Each individual biological sample wasqPCR-amplified in technical duplicate. Error bars are +/−SD. Expressiondata from drug treatments were normalized to GAPDH probe.

FIG. 7 shows electrospray ionization mass spectra of CDK12/CCNK complexafter treatment with DMSO for 1 hr at room temperature. The zero-chargemass spectra in the upper panel and inset is the result of deconvolutionof the raw mass spectrum in the lower panel. A, CCNK. C, phosphorylatedCDK12. D, CDK12.

FIG. 8 shows electrospray ionization mass spectra of CDK12/CCNK complexafter treatment with E-9 for 1 hr at room temperature. The zero-chargemass spectra in the upper panel and inset is the result of deconvolutionof the raw mass spectrum in the lower panel. A, CCNK. B, phosphorylatedand E-9 labeled CDK12. C, E-9 labeled CDK12. Only the masses of CDK12proteins shift after treatment.

FIG. 9 shows pull down assay with exemplified compounds. The first andsecond wells are at the concentrations of 1 μM and 200 nM respectively.

FIG. 10 shows KiNativ™ kinome profiling of compound E9.

FIG. 11 shows exemplified downstream genes. Transcription of thesedownstream genes are affected by the activities of CDK7, CDK12, andCDK13.

FIG. 12 shows an overview of the CRISPR-mediated strategy to introducecysteine-to-serine mutations into the genomic loci of CDK12 and CDK13.Shown are gene tracks of RNA polymerase II ChIP-seq signal at CDK12(left) and CDK13 (left) gene loci in Jurkat cells. Cartoons depict (1)the Cas9/guide RNA construct used to target Cas9-mediated DNA cutting toparticular either CDK12 or CDK/13 gene loci and (2) a repair constructthat contains DNA sequence encoding for a serine mutation in CDK12(C1039S) and CDK13 (C1017S), which together introduce the desiredcysteine-to-serine coding mutations into these loci.

FIG. 13 shows genotype for wild type (top) CDK12 C1039S/CDK13 C1017Sdouble mutant (bottom) cells. The sequencing results for CDK12 (left)and CDK13 (right) loci are depicted. Expression of these putativelyinhibitor-refractory mutants is expected to rescue compound-inducedproliferation defects that result from CDK12 and CDK13 covalentinhibition. For CDK12 WT loci, TGC codes for cysteine; while for CDK12C1039S loci, TCC codes for serine. For CDK13 WT loci, TGT codes forcysteine; while for CDK13 C1017S loci, TCT codes for serine.

FIG. 14 shows the 72 hour proliferation results from wild type and CDK12C1039S/CDK13 C1017S HAP1 cells. Double mutant cells are 4-fold lesssensitive to E17 compared to wild type cells indicating rescue ofCDK12/13 inhibition-induced proliferation defects. HAP1 cells wereseeded at a density of 12,000 cells/well in 96-well plates. Twenty-fourhours later, cells were treated with the indicated compounds in a 10-ptdose escalation format from 1 nM to 10 μM or DMSO control for 72 hours.After 72 hours, the cells were assayed using CellTiter-Glo LuminescentCell Viability Assay (Promega) to determine cell viability by measuringthe amount of ATP present in each sample cell population, which is anindicator of cell metabolic activity. Results were graphed as fractionof the DMSO control at 72 hours. All data points were performed inbiological triplicate. Error bars are +/−SD.

FIG. 15 shows the profiling of E-9 and E17 in the HAP1 cellproliferation assay. HAP1 cells expressing inhibitor-refractorymutations in CDK12 (C1039S) and CDK13 (C1017S) were 4-fold lesssensitive to E17 compared to control wild type HAP1 cells. This resultindicates that a significant portion of intracellular E17 activity comesfrom covalent inhibition of CDK12 and/or CDK13. Mutation of thesetargeted cysteines to a less nucleophilic serine is sufficient to rescuea significant portion of anti-proliferative activity at concentrationsless than 350 nM.

DEFINITIONS

Definitions of specific functional groups and chemical terms aredescribed in more detail below. The chemical elements are identified inaccordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, andspecific functional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in ThomasSorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition,John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive OrganicTransformations, VCH Publishers, Inc., New York, 1989; and Carruthers,Some Modern Methods of Organic Synthesis, 3^(rd) Edition, CambridgeUniversity Press, Cambridge, 1987. The disclosure is not intended to belimited in any manner by the exemplary listing of substituents describedherein.

Compounds described herein can comprise one or more asymmetric centers,and thus can exist in various isomeric forms, e.g., enantiomers and/ordiastereomers. For example, the compounds described herein can be in theform of an individual enantiomer, diastereomer or geometric isomer, orcan be in the form of a mixture of stereoisomers, including racemicmixtures and mixtures enriched in one or more stereoisomer. Isomers canbe isolated from mixtures by methods known to those skilled in the art,including chiral high pressure liquid chromatography (HPLC) and theformation and crystallization of chiral salts; or preferred isomers canbe prepared by asymmetric syntheses. See, for example, Jacques et al.,Enantiomers, Racemates and Resolutions (Wiley Interscience, New York,1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistryof Carbon Compounds (McGraw-Hill, N Y, 1962); and Wilen, Tables ofResolving Agents and Optical Resolutions, p. 268 (E. L. Eliel, Ed.,Univ. of Notre Dame Press, Notre Dame, Ind. 1972). The disclosureadditionally encompasses compounds described herein as individualisomers substantially free of other isomers, and alternatively, asmixtures of various isomers.

In a formula,

is a single bond where the stereochemistry of the moieties immediatelyattached thereto is not specified, - - - is absent or a single bond, and

or

is a single or double bond.

Unless otherwise stated, structures depicted herein are also meant toinclude compounds that differ only in the presence of one or moreisotopically enriched atoms. For example, compounds having the presentstructures except for the replacement of hydrogen by deuterium ortritium, replacement of ¹⁹F with ¹⁸F, or the replacement of ¹²C with ¹³Cor ¹⁴C are within the scope of the disclosure. Such compounds areuseful, for example, as analytical tools or probes in biological assays.

When a range of values is listed, it is intended to encompass each valueand sub-range within the range. For example “C₁₋₆” is intended toencompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆,C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆.

The term “aliphatic” includes both saturated and unsaturated, straightchain (i.e., unbranched), branched, acyclic, cyclic, or polycyclicaliphatic hydrocarbons, which are optionally substituted with one ormore functional groups. As will be appreciated by one of ordinary skillin the art, “aliphatic” is intended herein to include, but is notlimited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, andcycloalkynyl moieties. Thus, the term “alkyl” includes straight,branched and cyclic alkyl groups. An analogous convention applies toother generic terms such as “alkenyl”, “alkynyl”, and the like.Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the likeencompass both substituted and unsubstituted groups. In certainembodiments, “lower alkyl” is used to indicate those alkyl groups(cyclic, acyclic, substituted, unsubstituted, branched or unbranched)having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employedin the disclosure contain 1-20 aliphatic carbon atoms. In certain otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-10 aliphatic carbon atoms. In yet otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-8 aliphatic carbon atoms. In still otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-6 aliphatic carbon atoms. In yet other embodiments,the alkyl, alkenyl, and alkynyl groups employed in the disclosurecontain 1-4 carbon atoms. Illustrative aliphatic groups thus include,but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl,cyclopropyl, —CH₂-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl,isobutyl, tert-butyl, cyclobutyl, —CH₂-cyclobutyl, n-pentyl, sec-pentyl,isopentyl, tert-pentyl, cyclopentyl, —CH₂-cyclopentyl, n-hexyl,sec-hexyl, cyclohexyl, —CH₂-cyclohexyl moieties and the like, whichagain, may bear one or more substituents. Alkenyl groups include, butare not limited to, for example, ethenyl, propenyl, butenyl,1-methyl-2-buten-1-yl, and the like. Representative alkynyl groupsinclude, but are not limited to, ethynyl, 2-propynyl (propargyl),1-propynyl, and the like.

The term “alkyl” refers to a radical of a straight-chain or branchedsaturated hydrocarbon group having from 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), propyl(C₃) (e.g., n-propyl, isopropyl), butyl (C₄) (e.g., n-butyl, tert-butyl,sec-butyl, iso-butyl), pentyl (C₅) (e.g., n-pentyl, 3-pentanyl, amyl,neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C₆) (e.g.,n-hexyl). Additional examples of alkyl groups include n-heptyl (C₇),n-octyl (C₈), and the like. Unless otherwise specified, each instance ofan alkyl group is independently unsubstituted (an “unsubstituted alkyl”)or substituted (a “substituted alkyl”) with one or more substituents(e.g., halogen, such as F). In certain embodiments, the alkyl group isan unsubstituted C₁₋₁₀ alkyl (such as unsubstituted C₁₋₆ alkyl, e.g.,—CH₃). In certain embodiments, the alkyl group is a substituted C₁₋₁₀alkyl (such as substituted C₁₋₆ alkyl, e.g., —CF₃). In certainembodiments, the alkyl group is unsubstituted C₁₋₁₀ alkyl (such asunsubstituted C₁₋₆ alkyl, e.g., —CH₃ (Me), unsubstituted ethyl (Et),unsubstituted propyl (Pr, e.g., unsubstituted n-propyl (n-Pr),unsubstituted isopropyl (i-Pr)), unsubstituted butyl (Bu, e.g.,unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl (tert-Bu ort-Bu), unsubstituted sec-butyl (sec-Bu), unsubstituted isobutyl (i-Bu)).In certain embodiments, the alkyl group is substituted C₁₋₁₀ alkyl (suchas substituted C₁₋₆ alkyl, e.g., —CF₃, Bn).

The term “haloalkyl” is a substituted alkyl group, wherein one or moreof the hydrogen atoms are independently replaced by a halogen, e.g.,fluoro, bromo, chloro, or iodo. In some embodiments, the haloalkylmoiety has 1 to 8 carbon atoms (“C₁₋₈ haloalkyl”). In some embodiments,the haloalkyl moiety has 1 to 6 carbon atoms (“C₁₋₆ haloalkyl”). In someembodiments, the haloalkyl moiety has 1 to 4 carbon atoms (“C₁₋₄haloalkyl”). In some embodiments, the haloalkyl moiety has 1 to 3 carbonatoms (“C₁₋₃ haloalkyl”). In some embodiments, the haloalkyl moiety has1 to 2 carbon atoms (“C₁₋₂ haloalkyl”). Examples of haloalkyl groupsinclude —CHF₂, —CH₂F, —CF₃, —CH₂CF₃, —CF₂CF₃, —CF₂CF₂CF₃, —CCl₃, CFCl₂,—CF₂Cl, and the like.

The term “heteroalkyl” refers to an alkyl group, which further includesat least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected fromoxygen, nitrogen, or sulfur within (i.e., inserted between adjacentcarbon atoms of) and/or placed at one or more terminal position(s) ofthe parent chain. In certain embodiments, a heteroalkyl group refers toa saturated group having from 1 to 10 carbon atoms and 1 or moreheteroatoms within the parent chain (“heteroC₁₋₁₀ alkyl”). In someembodiments, a heteroalkyl group is a saturated group having 1 to 9carbon atoms and 1 or more heteroatoms within the parent chain(“heteroC₁₋₉ alkyl”). In some embodiments, a heteroalkyl group is asaturated group having 1 to 8 carbon atoms and 1 or more heteroatomswithin the parent chain (“heteroC₁₋₈ alkyl”). In some embodiments, aheteroalkyl group is a saturated group having 1 to 7 carbon atoms and 1or more heteroatoms within the parent chain (“heteroC₁₋₇ alkyl”). Insome embodiments, a heteroalkyl group is a saturated group having 1 to 6carbon atoms and 1 or more heteroatoms within the parent chain(“heteroC₁₋₆ alkyl”). In some embodiments, a heteroalkyl group is asaturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms withinthe parent chain (“heteroC₁₋₅ alkyl”). In some embodiments, aheteroalkyl group is a saturated group having 1 to 4 carbon atoms andfor 2 heteroatoms within the parent chain (“heteroC₁₋₄ alkyl”). In someembodiments, a heteroalkyl group is a saturated group having 1 to 3carbon atoms and 1 heteroatom within the parent chain (“heteroC₁₋₃alkyl”). In some embodiments, a heteroalkyl group is a saturated grouphaving 1 to 2 carbon atoms and 1 heteroatom within the parent chain(“heteroC₁₋₂ alkyl”). In some embodiments, a heteroalkyl group is asaturated group having 1 carbon atom and 1 heteroatom (“heteroC₁alkyl”). In some embodiments, a heteroalkyl group is a saturated grouphaving 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parentchain (“heteroC₂₋₆ alkyl”). Unless otherwise specified, each instance ofa heteroalkyl group is independently unsubstituted (an “unsubstitutedheteroalkyl”) or substituted (a “substituted heteroalkyl”) with one ormore substituents. In certain embodiments, the heteroalkyl group isunsubstituted heteroC₁₋₁₀ alkyl. In certain embodiments, the heteroalkylgroup is substituted heteroC₁₋₁₀ alkyl.

“Alkenyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon double bonds, and no triple bonds (“C₂₋₂₀ alkenyl”). Insome embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms(“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenylgroup has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, analkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In someembodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”).In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂alkenyl”). The one or more carbon-carbon double bonds can be internal(such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples ofC₂₋₄ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl(C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like.Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenylgroups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and thelike. Additional examples of alkenyl include heptenyl (C₇), octenyl(C₈), octatrienyl (C₈), and the like. Unless otherwise specified, eachinstance of an alkenyl group is independently optionally substituted,i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certainembodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. Incertain embodiments, the alkenyl group is substituted C₂₋₁₀ alkenyl. Inan alkenyl group, a C═C double bond for which the stereochemistry is notspecified (e.g., —CH═CHCH₃ or

may be an (E)- or (Z)-double bond.

The term “heteroalkenyl” refers to an alkenyl group, which furtherincludes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms)selected from oxygen, nitrogen, and sulfur within (i.e., insertedbetween adjacent carbon atoms of) and/or placed at one or more terminalposition(s) of the parent chain. In certain embodiments, a heteroalkenylgroup refers to a group having from 2 to 10 carbon atoms, at least onedouble bond, and 1 or more heteroatoms within the parent chain(“heteroC₂₋₁₀ alkenyl”). In some embodiments, a heteroalkenyl group has2 to 9 carbon atoms at least one double bond, and 1 or more heteroatomswithin the parent chain (“heteroC₂₋₉ alkenyl”). In some embodiments, aheteroalkenyl group has 2 to 8 carbon atoms, at least one double bond,and 1 or more heteroatoms within the parent chain (“heteroC₂₋₈alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 7 carbonatoms, at least one double bond, and 1 or more heteroatoms within theparent chain (“heteroC₂₋₇ alkenyl”). In some embodiments, aheteroalkenyl group has 2 to 6 carbon atoms, at least one double bond,and 1 or more heteroatoms within the parent chain (“heteroC₂₋₆alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 5 carbonatoms, at least one double bond, and 1 or 2 heteroatoms within theparent chain (“heteroC₂₋₅ alkenyl”). In some embodiments, aheteroalkenyl group has 2 to 4 carbon atoms, at least one double bond,and for 2 heteroatoms within the parent chain (“heteroC₂₋₄ alkenyl”). Insome embodiments, a heteroalkenyl group has 2 to 3 carbon atoms, atleast one double bond, and 1 heteroatom within the parent chain(“heteroC₂₋₃ alkenyl”). In some embodiments, a heteroalkenyl group has 2to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatomswithin the parent chain (“heteroC₂₋₆ alkenyl”). Unless otherwisespecified, each instance of a heteroalkenyl group is independentlyunsubstituted (“unsubstituted heteroalkenyl”) or substituted(“substituted heteroalkenyl”) with one or more substituents. In certainembodiments, the heteroalkenyl group is unsubstituted heteroC₂₋₁₀alkenyl. In certain embodiments, the heteroalkenyl group is substitutedheteroC₂₋₁₀ alkenyl.

“Alkynyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon triple bonds, and optionally one or more double bonds(“C₂₋₂₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 10carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl grouphas 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, analkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In someembodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”).In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms(“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynylgroup has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbontriple bonds can be internal (such as in 2-butynyl) or terminal (such asin 1-butynyl). Examples of C₂₋₄ alkynyl groups include, withoutlimitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl(C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₆ alkenyl groupsinclude the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅),hexynyl (C₆), and the like. Additional examples of alkynyl includeheptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified,each instance of an alkynyl group is independently optionallysubstituted, i.e., unsubstituted (an “unsubstituted alkynyl”) orsubstituted (a “substituted alkynyl”) with one or more substituents. Incertain embodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl.In certain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

The term “heteroalkynyl” refers to an alkynyl group that includes atleast one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected fromoxygen, nitrogen, and sulfur within (i.e., inserted between adjacentcarbon atoms of) and/or placed at one or more terminal position(s) ofthe parent chain. In certain embodiments, a heteroalkynyl group refersto a group having from 2 to 10 carbon atoms, at least one triple bond,and 1 or more heteroatoms within the parent chain (“heteroC₂₋₁₀alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 9 carbonatoms, at least one triple bond, and 1 or more heteroatoms within theparent chain (“heteroC₂₋₉ alkynyl”). In some embodiments, aheteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond,and 1 or more heteroatoms within the parent chain (“heteroC₂₋₈alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 7 carbonatoms, at least one triple bond, and 1 or more heteroatoms within theparent chain (“heteroC₂₋₇ alkynyl”). In some embodiments, aheteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond,and 1 or more heteroatoms within the parent chain (“heteroC₂₋₆alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 5 carbonatoms, at least one triple bond, and 1 or 2 heteroatoms within theparent chain (“heteroC₂₋₅ alkynyl”). In some embodiments, aheteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond,and for 2 heteroatoms within the parent chain (“heteroC₂₋₄ alkynyl”). Insome embodiments, a heteroalkynyl group has 2 to 3 carbon atoms, atleast one triple bond, and 1 heteroatom within the parent chain(“heteroC₂₋₃ alkynyl”). In some embodiments, a heteroalkynyl group has 2to 6 carbon atoms, at least one triple bond, and 1 or 2 heteroatomswithin the parent chain (“heteroC₂₋₆ alkynyl”). Unless otherwisespecified, each instance of a heteroalkynyl group is independentlyunsubstituted (“unsubstituted heteroalkynyl”) or substituted(“substituted heteroalkynyl”) with one or more substituents. In certainembodiments, the heteroalkynyl group is unsubstituted heteroC₂₋₁₀alkynyl. In certain embodiments, the heteroalkynyl group is substitutedheteroC₂₋₁₀ alkynyl.

“Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromaticcyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. Insome embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms(“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, acarbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). Insome embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms(“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include,without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl(C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅),cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like.Exemplary C₃₋₈ carbocyclyl groups include, without limitation, theaforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇),cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇),cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇),bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclylgroups include, without limitation, the aforementioned C₃₋₈ carbocyclylgroups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀),cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl(C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examplesillustrate, in certain embodiments, the carbocyclyl group is eithermonocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged orspiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) andcan be saturated or can be partially unsaturated. “Carbocyclyl” alsoincludes ring systems wherein the carbocyclic ring, as defined above, isfused with one or more aryl or heteroaryl groups wherein the point ofattachment is on the carbocyclic ring, and in such instances, the numberof carbons continue to designate the number of carbons in thecarbocyclic ring system. Unless otherwise specified, each instance of acarbocyclyl group is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a“substituted carbocyclyl”) with one or more substituents. In certainembodiments, the carbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl.In certain embodiments, the carbocyclyl group is substituted C₃₋₁₀carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturatedcarbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ringcarbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkylgroup has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In someembodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ringcarbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groupsinclude cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups aswell as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups aswell as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwisespecified, each instance of a cycloalkyl group is independentlyunsubstituted (an “unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certainembodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. Incertain embodiments, the cycloalkyl group is substituted C₃₋₁₀cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to10-membered non-aromatic ring system having ring carbon atoms and 1 to 4ring heteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 memberedheterocyclyl”). In heterocyclyl groups that contain one or more nitrogenatoms, the point of attachment can be a carbon or nitrogen atom, asvalency permits. A heterocyclyl group can either be monocyclic(“monocyclic heterocyclyl”) or a fused, bridged, or spiro ring system,such as a bicyclic system (“bicyclic heterocyclyl”), and can besaturated or can be partially unsaturated. Heterocyclyl bicyclic ringsystems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring,as defined above, is fused with one or more carbocyclyl groups whereinthe point of attachment is either on the carbocyclyl or heterocyclicring, or ring systems wherein the heterocyclic ring, as defined above,is fused with one or more aryl or heteroaryl groups, wherein the pointof attachment is on the heterocyclic ring, and in such instances, thenumber of ring members continue to designate the number of ring membersin the heterocyclic ring system. Unless otherwise specified, eachinstance of heterocyclyl is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certainembodiments, the heterocyclyl group is unsubstituted 3-10 memberedheterocyclyl. In certain embodiments, the heterocyclyl group issubstituted 3-10 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 membered,non-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 memberedheterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8membered non-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In someembodiments, a heterocyclyl group is a 5-6 membered non-aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms, wherein eachheteroatom is independently selected from nitrogen, oxygen, and sulfur(“5-6 membered heterocyclyl”). In some embodiments, the 5-6 memberedheterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen,and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2ring heteroatoms selected from nitrogen, oxygen, and sulfur. In someembodiments, the 5-6 membered heterocyclyl has one ring heteroatomselected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing one heteroatominclude, without limitation, azirdinyl, oxiranyl, thiiranyl. Exemplary4-membered heterocyclyl groups containing one heteroatom include,without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary5-membered heterocyclyl groups containing one heteroatom include,without limitation, tetrahydrofuranyl, dihydrofuranyl,tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl,and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groupscontaining two heteroatoms include, without limitation, dioxolanyl,oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-memberedheterocyclyl groups containing three heteroatoms include, withoutlimitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary6-membered heterocyclyl groups containing one heteroatom include,without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl,and thianyl. Exemplary 6-membered heterocyclyl groups containing twoheteroatoms include, without limitation, piperazinyl, morpholinyl,dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groupscontaining three heteroatoms include, without limitation, triazinanyl.Exemplary 7-membered heterocyclyl groups containing one heteroatominclude, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary8-membered heterocyclyl groups containing one heteroatom include,without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary5-membered heterocyclyl groups fused to a C₆ aryl ring (also referred toherein as a 5,6-bicyclic heterocyclic ring) include, without limitation,indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groupsfused to an aryl ring (also referred to herein as a 6,6-bicyclicheterocyclic ring) include, without limitation, tetrahydroquinolinyl,tetrahydroisoquinolinyl, and the like. Exemplary bicyclic heterocyclylgroups include, without limitation, indolinyl, isoindolinyl,dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl,tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl,tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl,octahydrochromenyl, octahydroisochromenyl, decahydronaphthyridinyl,decahydro-1,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl,phthalimidyl, naphthalimidyl, chromanyl, chromenyl,1H-benzo[e][1,4]diazepinyl, 1,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl,5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro-5H-furo[3,2-b]pyranyl,5,7-dihydro-4H-thieno[2,3-c]pyranyl,2,3-dihydro-1H-pyrrolo[2,3-b]pyridinyl, 2,3-dihydrofuro[2,3-b]pyridinyl,4,5,6,7-tetrahydro-1H-pyrrolo[2,3-b]pyridinyl,4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl,4,5,6,7-tetrahydrothieno[3,2-b]pyridinyl,1,2,3,4-tetrahydro-1,6-naphthyridinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclicor tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 pielectrons shared in a cyclic array) having 6-14 ring carbon atoms andzero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). Insome embodiments, an aryl group has six ring carbon atoms (“C₆ aryl”;e.g., phenyl). In some embodiments, an aryl group has ten ring carbonatoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). Insome embodiments, an aryl group has fourteen ring carbon atoms (“C₁₄aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein thearyl ring, as defined above, is fused with one or more carbocyclyl orheterocyclyl groups, wherein the radical or point of attachment is onthe aryl ring, and in such instances, the number of carbon atomscontinue to designate the number of carbon atoms in the aryl ringsystem. Unless otherwise specified, each instance of an aryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted aryl”) or substituted (a “substituted aryl”) with one ormore substituents. In certain embodiments, the aryl group isunsubstituted C₆₋₁₄ aryl. In certain embodiments, the aryl group issubstituted C₆₋₁₄ aryl.

“Aralkyl” refers to an optionally substituted alkyl group substituted byan optionally substituted aryl group. “Aralkyl” is a subset of “alkyl”and refers to an alkyl group substituted with an aryl group, wherein thepoint of attachment is on the alkyl group. In certain embodiments, thearalkyl is optionally substituted benzyl. In certain embodiments, thearalkyl is benzyl. In certain embodiments, the aralkyl is optionallysubstituted phenethyl. In certain embodiments, the aralkyl is phenethyl.

“Heteroaryl” refers to a radical of a 5-10 membered, monocyclic orbicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 pi electronsshared in a cyclic array) having ring carbon atoms and 1-4 ringheteroatoms provided in the aromatic ring system, wherein eachheteroatom is independently selected from nitrogen, oxygen and sulfur(“5-10 membered heteroaryl”). In heteroaryl groups that contain one ormore nitrogen atoms, the point of attachment can be a carbon or nitrogenatom, as valency permits. Heteroaryl bicyclic ring systems can includeone or more heteroatoms in one or both rings. “Heteroaryl” includes ringsystems wherein the heteroaryl ring, as defined above, is fused with oneor more carbocyclyl or heterocyclyl groups wherein the point ofattachment is on the heteroaryl ring, and in such instances, the numberof ring members continue to designate the number of ring members in theheteroaryl ring system. “Heteroaryl” also includes ring systems whereinthe heteroaryl ring, as defined above, is fused with one or more arylgroups wherein the point of attachment is either on the aryl orheteroaryl ring, and in such instances, the number of ring membersdesignates the number of ring members in the fused (aryl/heteroaryl)ring system. Bicyclic heteroaryl groups wherein one ring does notcontain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and thelike) the point of attachment can be on either ring, i.e., either thering bearing a heteroatom (e.g., 2-indolyl) or the ring that does notcontain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”)with one or more substituents. In certain embodiments, the heteroarylgroup is unsubstituted 5-14 membered heteroaryl. In certain embodiments,the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatominclude, without limitation, pyrrolyl, furanyl, and thiophenyl.Exemplary 5-membered heteroaryl groups containing two heteroatomsinclude, without limitation, imidazolyl, pyrazolyl, oxazolyl,isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroarylgroups containing three heteroatoms include, without limitation,triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-memberedheteroaryl groups containing four heteroatoms include, withoutlimitation, tetrazolyl. Exemplary 6-membered heteroaryl groupscontaining one heteroatom include, without limitation, pyridinyl.Exemplary 6-membered heteroaryl groups containing two heteroatomsinclude, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.Exemplary 6-membered heteroaryl groups containing three or fourheteroatoms include, without limitation, triazinyl and tetrazinyl,respectively. Exemplary 7-membered heteroaryl groups containing oneheteroatom include, without limitation, azepinyl, oxepinyl, andthiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, withoutlimitation, indolyl, isoindolyl, indazolyl, benzotriazolyl,benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl,benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl,benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, andpurinyl. Exemplary 6,6-bicyclic heteroaryl groups include, withoutlimitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplarytricyclic heteroaryl groups include, without limitation,phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl,phenoxazinyl, and phenazinyl.

“Heteroaralkyl” is a subset of alkyl and heteroaryl and refers to anoptionally substituted alkyl group substituted by an optionallysubstituted heteroaryl group.

“Unsaturated” or “partially unsaturated” refers to a group that includesat least one double or triple bond. A “partially unsaturated” ringsystem is further intended to encompass rings having multiple sites ofunsaturation, but is not intended to include aromatic groups (e.g., arylor heteroaryl groups). Likewise, “saturated” refers to a group that doesnot contain a double or triple bond, i.e., contains all single bonds.

The term “unsaturated bond” refers to a double or triple bond.

The term “unsaturated” or “partially unsaturated” refers to a moietythat includes at least one double or triple bond.

The term “saturated” refers to a moiety that does not contain a doubleor triple bond, i.e., the moiety only contains single bonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, which are divalent linking groups, are further referred to usingthe suffix -ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene,heterocyclylene, arylene, and heteroarylene. Thus, alkylene is thedivalent moiety of alkyl, alkenylene is the divalent moiety of alkenyl,alkynylene is the divalent moiety of alkynyl, heteroalkylene is thedivalent moiety of heteroalkyl, heteroalkenylene is the divalent moietyof heteroalkenyl, heteroalkynylene is the divalent moiety ofheteroalkynyl, carbocyclylene is the divalent moiety of carbocyclyl,heterocyclylene is the divalent moiety of heterocyclyl, arylene is thedivalent moiety of aryl, and heteroarylene is the divalent moiety ofheteroaryl.

An atom, moiety, or group described herein may be unsubstituted orsubstituted, as valency permits, unless otherwise provided expressly.The term “optionally substituted” refers to substituted orunsubstituted.

A group is optionally substituted unless expressly provided otherwise.The term “optionally substituted” refers to being substituted orunsubstituted. In certain embodiments, alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are optionallysubstituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted”or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl,“substituted” or “unsubstituted” carbocyclyl, “substituted” or“unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or“substituted” or “unsubstituted” heteroaryl group). In general, the term“substituted”, whether preceded by the term “optionally” or not, meansthat at least one hydrogen present on a group (e.g., a carbon ornitrogen atom) is replaced with a permissible substituent, e.g., asubstituent which upon substitution results in a stable compound, e.g.,a compound which does not spontaneously undergo transformation such asby rearrangement, cyclization, elimination, or other reaction. Unlessotherwise indicated, a “substituted” group has a substituent at one ormore substitutable positions of the group, and when more than oneposition in any given structure is substituted, the substituent iseither the same or different at each position. The term “substituted” iscontemplated to include substitution with all permissible substituentsof organic compounds, any of the substituents described herein thatresults in the formation of a stable compound. The present disclosurecontemplates any and all such combinations in order to arrive at astable compound. For purposes of this disclosure, heteroatoms such asnitrogen may have hydrogen substituents and/or any suitable substituentas described herein which satisfy the valencies of the heteroatoms andresults in the formation of a stable moiety. In certain embodiments, thesubstituent is a carbon atom substituent. In certain embodiments, thesubstituent is a nitrogen atom substituent. In certain embodiments, thesubstituent is an oxygen atom substituent. In certain embodiments, thesubstituent is a sulfur atom substituent.

Exemplary carbon atom substituents include, but are not limited to,halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂,—N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa),—SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂,—NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂,—NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa),—S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃, —OSi(R^(aa))₃,—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa), —SC(═S)SR^(aa),—SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa), —SC(═O)R^(aa),—P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂,—P(═O)(N(R^(bb))₂)₂, —OP(═O)(N(R^(bb))₂)₂, —NR^(bb)P(═O)(R^(aa))₂,—NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(N(R^(bb))₂)₂, —P(R^(cc))₂,—P(OR^(cc))₂, —P(R^(cc))₃ ⁺X⁻, —P(OR^(cc))₃ ⁺X⁻, —P(R^(cc))₄,—P(OR^(cc))₄, —OP(R^(cc))₂, —OP(R^(cc))₃ ⁺X⁻, —OP(OR^(cc))₂,—OP(OR^(cc))₃ ⁺X⁻, —OP(R^(cc))₄, —OP(OR^(cc))₄, —B(R^(aa))₂,—B(OR^(cc))₂, —BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀alkenyl, C₂₋₁₀ alkynyl, heteroC₁₋₁₀ alkyl, heteroC₂₋₁₀ alkenyl,heteroC₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl,C₆₋₁₄ aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl,alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups; or twogeminal hydrogens on a carbon atom are replaced with the group ═O, ═S,═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa),═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc); wherein X⁻ is acounterion;

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(aa) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH,—OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂,—SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc),—C(═S)SR^(cc), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)(N(R^(cc))₂)₂,C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl,heteroC₁₋₁₀alkyl, heteroC₂₋₁₀alkenyl, heteroC₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(bb) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;wherein X⁻ is a counterion;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

-   -   each instance of R^(dd) is, independently, selected from        halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee),        —ON(R^(ff))₂, —N(R^(ff))₂, —N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff),        —SH, —SR^(ee), —SSR^(ee), —C(═O)R^(cc), —CO₂H, —CO₂R^(ee),        —OC(═O)R^(ee), —OCO₂R^(ee), —C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂,        —NR^(ff)C(═O)R^(ee), —NR^(ff)CO₂R^(ee), —NR^(ff)C(═O)N(R^(ff))₂,        —C(═NR^(ff))OR^(cc), —OC(═NR^(ff))R^(cc), —OC(═NR^(ff))OR^(ee),        —C(═NR^(ff))N(R^(ff))₂, —OC(═NR^(ff))N(R^(ff))₂,        —NR^(ff)C(═NR^(ff))N(R^(ff))₂, —NR^(ff)SO₂R^(ee),        —SO₂N(R^(ff))₂, —SO₂R^(ee), —SO₂OR^(ee), —OSO₂R^(ee),        —S(═O)R^(ee), —Si(R^(ee))₃, —OSi(R^(ee))₃, —C(═S)N(R^(ff))₂,        —C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O) (OR^(ee))₂,        —P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆        alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀        carbocyclyl, 3-10 membered heterocyclyl, C₆₋₁₀ aryl, 5-10        membered heteroaryl, wherein each alkyl, alkenyl, alkynyl,        carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently        substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups, or two        geminal R^(dd) substituents can be joined to form ═O or ═S;        wherein X⁻ is a counterion;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl,C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, ortwo R^(ff) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃,—SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl),—N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆ alkyl)⁺X⁻, —NH₃⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SH,—SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —CO₂(C₁₋₆alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆alkyl)C(═O)(C₁₋₆ alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl),—NHC(═O)NH(C₁₋₆ alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆alkyl), —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl), —C(═NH)NH(C₁₋₆alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl),—OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl), —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl),—SO₂N(C₁₋₆ alkyl), —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl,—SO₂₀C₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl, —SOC₁₋₆ alkyl, —Si(C₁₋₆ alkyl)₃,—OSi(C₁₋₆ alkyl)₃-C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂,—C(═O)S(C₁₋₆ alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)(OC₁₋₆ alkyl)₂, —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 memberedheteroaryl; or two geminal R^(gg) substituents can be joined to form ═Oor ═S; wherein X⁻ is a counterion.

A “counterion” or “anionic counterion” is a negatively charged groupassociated with a cationic quaternary amino group in order to maintainelectronic neutrality. Exemplary counterions include halide ions (e.g.,F⁻, Cl⁻, Br⁻, I⁻), NO₃ ⁻, ClO₄ ⁻, OH⁻, H₂PO₄ ⁻, HSO₄ ⁻, sulfonate ions(e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate,benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate,naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonicacid-2-sulfonate, and the like), carboxylate ions (e.g., acetate,ethanoate, propanoate, benzoate, glycerate, lactate, tartrate,glycolate, and the like). Exemplary counterions further include BF₄ ⁻,PF₄ ⁻, PF₆ ⁻, AsF₆ ⁻, SbF₆ ⁻, B[3,5-(CF₃)₂C₆H₃]₄]⁻, B(C₆F₅)₄ ⁻, BPh₄ ⁻,Al(OC(CF₃)₃)₄ ⁻, and carborane anions (e.g., CB₁₁H_(R) ⁻ or(HCB₁₁Me₅Br₆)⁻). Exemplary counterions which may be multivalent includeCO₃ ²⁻, HPO₄ ²⁻, PO₄ ³⁻, B₄O₇ ²⁻, SO₄ ²⁻, S₂O₃ ²⁻, carboxylate anions(e.g., tartrate, citrate, fumarate, maleate, malate, malonate,gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate,sebacate, salicylate, phthalates, aspartate, glutamate, and the like),and carboranes.

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro,—Cl), bromine (bromo, —Br), or iodine (iodo, —I).

The term “hydroxyl” or “hydroxy” refers to the group —OH. The term“substituted hydroxyl” or “substituted hydroxyl,” by extension, refersto a hydroxyl group wherein the oxygen atom directly attached to theparent molecule is substituted with a group other than hydrogen, andincludes groups selected from —OR^(aa), —ON(R^(bb))₂, —OC(═O)SR^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —OC(═O)N(R^(bb))₂, —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —OC(═NR^(bb))N(R^(bb))₂, —OS(═O)R^(aa),—OSO₂R^(aa), —OSi(R^(aa))₃, —OP(R^(cc))₂, —OP(R^(cc))₃ ⁺X⁻,—OP(OR^(cc))₂, —OP(OR^(cc))₃ ⁺X⁻, —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂,and —OP(═O)(N(R^(bb)))₂, wherein X⁻, R^(aa), R^(bb), and R^(cc) are asdefined herein.

The term “amino” refers to the group —NH₂. The term “substituted amino,”by extension, refers to a monosubstituted amino, disubstituted amino, ortrisubstituted amino. In certain embodiments, the “substituted amino” isa monosubstituted amino or disubstituted amino group.

The term “sulfonyl” refers to a group selected from —SO₂N(R^(bb))₂,—SO₂R^(aa), and —SO₂OR^(aa), wherein R^(aa) and R^(bb) are as definedherein.

The term “sulfinyl” refers to the group —S(═O)R^(aa), wherein R^(aa) isas defined herein.

“Acyl” refers to a moiety selected from the group consisting of—C(═O)R^(aa), —CHO, —CO₂R^(aa), —C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa),—C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), or —C(═S)SR^(aa), wherein R^(aa) andR^(bb) are as defined herein. In other instances, “acyl” refers to agroup having the general formula: —C(═O)R^(X1), —C(═O)OR^(X1),—C(═O)—O—C(═O)R^(X1), —C(═O)SR^(X1), —C(═O)N(R^(X1))₂, —C(═S)R^(X1),—C(═S)N(R^(X1))₂, —C(═S)S(R^(X1)), —C(═NR^(X1))R^(X1),—C(═NR^(X1))OR^(X1), —C(═NR^(X1))SR^(X1), or —C(═NR^(X1))N(R^(X1))₂,wherein R^(X1) is hydrogen; halogen; substituted or unsubstitutedhydroxyl; substituted or unsubstituted thiol; substituted orunsubstituted amino; substituted or unsubstituted acyl, cyclic oracyclic, substituted or unsubstituted, branched or unbranched aliphatic;cyclic or acyclic, substituted or unsubstituted, branched or unbranchedheteroaliphatic; cyclic or acyclic, substituted or unsubstituted,branched or unbranched alkyl; cyclic or acyclic, substituted orunsubstituted, branched or unbranched alkenyl; substituted orunsubstituted alkynyl; substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, aliphaticoxy, heteroaliphaticoxy, alkyloxy,heteroalkyloxy, aryloxy, heteroaryloxy, aliphaticthioxy,heteroaliphaticthioxy, alkylthioxy, heteroalkylthioxy, arylthioxy,heteroarylthioxy, mono- or di-aliphaticamino, mono- ordi-heteroaliphaticamino, mono- or di-alkylamino, mono- ordi-heteroalkylamino, mono- or di-arylamino, or mono- ordi-heteroarylamino; or two R^(X1) groups taken together form a 5- to6-membered heterocyclic ring. Exemplary acyl groups include aldehydes(—CHO), carboxylic acids (—CO₂H), ketones, acyl halides, esters, amides,imines, carbonates, carbamates, and ureas. Acyl substituents include,but are not limited to, any of the substituents described herein, thatresult in the formation of a stable moiety (e.g., aliphatic, alkyl,alkenyl, alkynyl, heteroaliphatic, heterocyclic, aryl, heteroaryl, acyl,oxo, imino, thiooxo, cyano, isocyano, amino, azido, nitro, hydroxyl,thiol, halo, aliphaticamino, heteroaliphaticamino, alkylamino,heteroalkylamino, arylamino, heteroarylamino, alkylaryl, arylalkyl,aliphaticoxy, heteroaliphaticoxy, alkyloxy, heteroalkyloxy, aryloxy,heteroaryloxy, aliphaticthioxy, heteroaliphaticthioxy, alkylthioxy,heteroalkylthioxy, arylthioxy, heteroarylthioxy, acyloxy, and the like,each of which may or may not be further substituted).

The term “carbonyl” refers a group wherein the carbon directly attachedto the parent molecule is sp² hybridized, and is substituted with anoxygen, nitrogen, or sulfur atom, e.g., a group selected from ketones(—C(═O)R^(aa)), carboxylic acids (—CO₂H), aldehydes (—CHO), esters(—CO₂R^(aa), —C(═O)SR^(aa), —C(═S)SR^(aa)), amides (—C(═O)N(R^(bb))₂,—C(═O)NR^(bb)SO₂R^(aa), —C(═S)N(R^(bb))₂), and imines(—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa)), —C(═NR^(bb))N(R^(bb))₂),wherein R^(aa) and R^(bb) are as defined herein.

The term “silyl” refers to the group —Si(R^(aa))₃, wherein R^(aa) is asdefined herein.

The term “oxo” refers to the group ═O, and the term “thiooxo” refers tothe group ═S.

Nitrogen atoms can be substituted or unsubstituted as valency permits,and include primary, secondary, tertiary, and quaternary nitrogen atoms.Exemplary nitrogen atom substituents include, but are not limited to,hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa),—C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa),—C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc),—SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc),—P(═O) (OR^(cc))₂, —P(═O)(R^(aa))₂, —P(═O)(N(R^(cc))₂)₂, C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(cc) groups attached to a nitrogen atom are joined to form a 3-14membered heterocyclyl or 5-14 membered heteroaryl ring, wherein eachalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylis independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, andwherein R^(aa), R^(bb), R^(cc), and R^(dd) are as defined above.

In certain embodiments, the substituent present on a nitrogen atom is anitrogen protecting group (also referred to as an amino protectinggroup). Nitrogen protecting groups include, but are not limited to, —OH,—OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa),—C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc),—SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl(e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aralkyl, aryl, and heteroaryl is independently substitutedwith 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb),R^(cc) and R^(dd) are as defined herein. Nitrogen protecting groups arewell known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

For example, nitrogen protecting groups such as amide groups (e.g.,—C(═O)R^(aa)) include, but are not limited to, formamide, acetamide,chloroacetamide, trichloroacetamide, trifluoroacetamide,phenylacetamide, 3-phenylpropanamide, picolinamide,3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide,p-phenylbenzamide, o-nitrophenylacetamide, o-nitrophenoxyacetamide,acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide,3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,2-methyl-2-(o-nitrophenoxy)propanamide,2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethioninederivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g.,—C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethylcarbamate, 9-fluorenylmethyl carbamate (Fmoc),9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethylcarbamate,2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methylcarbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate(Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethylcarbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate,1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC),1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC),1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethylcarbamate, t-butyl carbamate (BOC or Boc), 1-adamantyl carbamate (Adoc),vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallylcarbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate(Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithiocarbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),p-nitrobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzylcarbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate,2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate,2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methylcarbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc),2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate(Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc),1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate,p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate,2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenylcarbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate,3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methylcarbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzylcarbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentylcarbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate,2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzylcarbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,2-furanylmethyl carbamate, 2-iodoethyl carbamate, isobornyl carbamate,isobutyl carbamate, isonicotinyl carbamate,p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate,1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate,1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate,p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate,4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzylcarbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g.,—S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide(Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide(Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb),2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide(Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide(Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide,4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to,phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacylderivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanylderivative, N-acetylmethionine derivative,4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts),N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole,N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE),5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine,N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammoniumsalts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),N-9-phenylfluorenylamine (PhF),N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm),N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine,N-benzylideneamine, N-p-methoxybenzylideneamine,N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine,N-p-nitrobenzylideneamine, N-salicylideneamine,N-5-chlorosalicylideneamine,N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine,N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,N-borane derivative, N-diphenylborinic acid derivative,N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate,N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide,diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt),diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzylphosphoramidate, diphenyl phosphoramidate, benzenesulfenamide,o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide,pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).

Exemplary oxygen atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃ ⁺X⁻,—P(OR^(cc))₂, —P(OR^(cc))₃ ⁺X⁻, —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, and—P(═O)(N(R^(bb))₂)₂, wherein X⁻, R^(aa), R^(bb), and R^(cc) are asdefined herein. In certain embodiments, the oxygen atom substituentpresent on an oxygen atom is an oxygen protecting group (also referredto as a hydroxyl protecting group). Oxygen protecting groups are wellknown in the art and include those described in detail in ProtectingGroups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd)edition, John Wiley & Sons, 1999, incorporated herein by reference.Exemplary oxygen protecting groups include, but are not limited to,methyl, t-butyloxycarbonyl (BOC or Boc), methoxylmethyl (MOM),methylthiomethyl (MTM), t-butylthiomethyl,(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM),p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM),guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM),siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl,bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR),tetrahydropyranyl (THP), 3-bromotetrahydropyranyl,tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl(MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranylS,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl(CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl,t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl,benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl,p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl,p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido,diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl,triphenylmethyl, α-naphthyldiphenylmethyl,p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl,tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl,4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl,4,4′,4″-tris(levulinoyloxyphenyl)methyl,4,4′,4″-tris(benzoyloxyphenyl)methyl,3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl,1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl,9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl(TMS), triethylsilyl (TES), triisopropylsilyl (TIPS),dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS),dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl(TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate,benzoylformate, acetate, chloroacetate, dichloroacetate,trichloroacetate, trifluoroacetate, methoxyacetate,triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate,3-phenylpropionate, 4-oxopentanoate (levulinate),4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate,adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate,2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate(TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec),2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutylcarbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkylp-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzylcarbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzylcarbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate,4-ethoxy-1-naphthyl carbonate, methyl dithiocarbonate, 2-iodobenzoate,4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,2,6-dichloro-4-methylphenoxyacetate,2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate,o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkylN,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate(Ts).

Exemplary sulfur atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)_(N)(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃,—P(R^(cc))₃ ⁺X⁻, —P(OR^(cc))₂, —P(OR^(cc))₃ ⁺X⁻, —P(═O)(R^(aa))₂,—P(═O)(OR^(cc))₂, and —P(═O)(N(R^(bb))₂)₂, wherein R^(aa), R^(bb), andR^(cc) are as defined herein. In certain embodiments, the sulfur atomsubstituent present on a sulfur atom is a sulfur protecting group (alsoreferred to as a thiol protecting group). Sulfur protecting groups arewell known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

A “hydrocarbon chain” refers to a substituted or unsubstituted divalentalkyl, alkenyl, or alkynyl group. A hydrocarbon chain includes (1) oneor more chains of carbon atoms immediately between the two radicals ofthe hydrocarbon chain; (2) optionally one or more hydrogen atoms on thechain(s) of carbon atoms; and (3) optionally one or more substituents(“non-chain substituents,” which are not hydrogen) on the chain(s) ofcarbon atoms. A chain of carbon atoms consists of consecutivelyconnected carbon atoms (“chain atoms” or “carbon units”) and does notinclude hydrogen atoms or heteroatoms. However, a non-chain substituentof a hydrocarbon chain may include any atoms, including hydrogen atoms,carbon atoms, and heteroatoms. For example, hydrocarbon chain—C^(A)H(C^(B)H₂C^(c)H₃)— includes one chain atom C^(A), one hydrogenatom on C^(A), and non-chain substituent —(C^(B)H₂C^(c)H₃). The term“C_(x) hydrocarbon chain,” wherein x is a positive integer, refers to ahydrocarbon chain that includes x number of chain atom(s) between thetwo radicals of the hydrocarbon chain. If there is more than onepossible value of x, the smallest possible value of x is used for thedefinition of the hydrocarbon chain. For example, —CH(C₂H₅)— is a C₁hydrocarbon chain, and

is a C₃ hydrocarbon chain. When a range of values is used, the meaningof the range is as described herein. For example, a C₃₋₁₀ hydrocarbonchain refers to a hydrocarbon chain where the number of chain atoms ofthe shortest chain of carbon atoms immediately between the two radicalsof the hydrocarbon chain is 3, 4, 5, 6, 7, 8, 9, or 10. A hydrocarbonchain may be saturated (e.g., —(CH₂)₄—). A hydrocarbon chain may also beunsaturated and include one or more C═C and/or CC bonds anywhere in thehydrocarbon chain. For instance, —CH═CH—(CH₂)₂—, —CH₂—C≡C—CH₂—, and—C≡C—CH═CH— are all examples of a unsubstituted and unsaturatedhydrocarbon chain. In certain embodiments, the hydrocarbon chain isunsubstituted (e.g., —C≡C— or —(CH₂)₄—). In certain embodiments, thehydrocarbon chain is substituted (e.g., —CH(C₂H₅)— and —CF₂—). Any twosubstituents on the hydrocarbon chain may be joined to form anoptionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, or optionally substituted heteroaryl ring.For instance,

are all examples of a hydrocarbon chain. In contrast, in certainembodiments,

are not within the scope of the hydrocarbon chains described herein.When a chain atom of a C, hydrocarbon chain is replaced with aheteroatom, the resulting group is referred to as a C, hydrocarbon chainwherein a chain atom is replaced with a heteroatom, as opposed to aC_(x−1) hydrocarbon chain. For example,

is a C₃ hydrocarbon chain wherein one chain atom is replaced with anoxygen atom.

The term “leaving group” is given its ordinary meaning in the art ofsynthetic organic chemistry and refers to an atom or a group capable ofbeing displaced by a nucleophile. Examples of suitable leaving groupsinclude, but are not limited to, halogen (such as F, Cl, Br, or I(iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy,arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy,aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, and haloformates. Insome cases, the leaving group is a sulfonic acid ester, such astoluenesulfonate (tosylate, —OTs), methanesulfonate (mesylate, —OMs),p-bromobenzenesulfonyloxy (brosylate, —OBs), —OS(═O)₂(CF₂)₃CF₃(nonaflate, —ONf), or trifluoromethanesulfonate (triflate, —OTf). Insome cases, the leaving group is a brosylate, such asp-bromobenzenesulfonyloxy. In some cases, the leaving group is anosylate, such as 2-nitrobenzenesulfonyloxy. The leaving group may alsobe a phosphineoxide (e.g., formed during a Mitsunobu reaction) or aninternal leaving group such as an epoxide or cyclic sulfate. Othernon-limiting examples of leaving groups are water, ammonia, alcohols,ether moieties, thioether moieties, zinc halides, magnesium moieties,diazonium salts, and copper moieties. Other exemplary leaving groupsinclude, but are not limited to, activated substituted hydroxyl groups(e.g., —OC(═O)SR^(aa), —OC(═O)R^(aa), —OCO₂R^(aa), —OC(═O)N(R^(bb))₂,—OC(═NR^(bb))R^(aa), —OC(═NR^(bb))OR^(aa), —OC(═NR^(bb))N(R^(bb))₂,—OS(═O)R^(aa), —OSO₂R^(aa), —OP(R^(cc))₂, —OP(R^(cc))₃, —OP(═O)₂R^(aa),—OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —OP(═O)₂N(R^(bb))₂, and—OP(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein).

The term “heteroatom” refers to an atom that is not hydrogen or carbon.In certain embodiments, the heteroatom is nitrogen. In certainembodiments, the heteroatom is oxygen. In certain embodiments, theheteroatom is sulfur.

As used herein, the term “salt” refers to any and all salts, andencompasses pharmaceutically acceptable salts. The term “salt” refers toionic compounds that result from the neutralization reaction of an acidand a base. A salt is composed of one or more cations (positivelycharged ions) and one or more anions (negative ions) so that the salt iselectrically neutral (without a net charge). Salts of the compounds ofthis invention include those derived from inorganic and organic acidsand bases. Examples of acid addition salts are salts of an amino groupformed with inorganic acids, such as hydrochloric acid, hydrobromicacid, phosphoric acid, sulfuric acid, and perchloric acid, or withorganic acids, such as acetic acid, oxalic acid, maleic acid, tartaricacid, citric acid, succinic acid, or malonic acid or by using othermethods known in the art such as ion exchange. Other salts includeadipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate,bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate, hippurate, andthe like. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium and N⁺ (C₁₋₄ alkyl)₄ salts.Representative alkali or alkaline earth metal salts include sodium,lithium, potassium, calcium, magnesium, and the like. Further saltsinclude ammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, lower alkyl sulfonate, and aryl sulfonate.

The term “pharmaceutically acceptable salt” refers to those salts whichare, within the scope of sound medical judgment, suitable for use incontact with the tissues of humans and lower animals without unduetoxicity, irritation, allergic response, and the like, and arecommensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, Berge et al.describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein byreference. Pharmaceutically acceptable salts of the compounds describedherein include those derived from suitable inorganic and organic acidsand bases. Examples of pharmaceutically acceptable, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid, and perchloric acid or with organic acids such as acetic acid,oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, ormalonic acid or by using other methods known in the art such as ionexchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium and N⁺ (C₁₋₄ alkyl)₄ ⁻ salts.Representative alkali or alkaline earth metal salts include sodium,lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, lower alkyl sulfonate, and aryl sulfonate.

The term “solvate” refers to forms of the compound that are associatedwith a solvent, usually by a solvolysis reaction. This physicalassociation may include hydrogen bonding. Conventional solvents includewater, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and thelike. The compounds described herein may be prepared, e.g., incrystalline form, and may be solvated. Suitable solvates includepharmaceutically acceptable solvates and further include bothstoichiometric solvates and non-stoichiometric solvates. In certaininstances, the solvate will be capable of isolation, for example, whenone or more solvent molecules are incorporated in the crystal lattice ofa crystalline solid. “Solvate” encompasses both solution-phase andisolatable solvates. Representative solvates include hydrates,ethanolates, and methanolates.

The term “hydrate” refers to a compound that is associated with water.Typically, the number of the water molecules contained in a hydrate of acompound is in a definite ratio to the number of the compound moleculesin the hydrate. Therefore, a hydrate of a compound may be represented,for example, by the general formula R.x H₂O, wherein R is the compound,and x is a number greater than 0. A given compound may form more thanone type of hydrate, including, e.g., monohydrates (x is 1), lowerhydrates (x is a number greater than 0 and smaller than 1, e.g.,hemihydrates (R.0.5H₂O)), and polyhydrates (x is a number greater than1, e.g., dihydrates (R.2 H₂O) and hexahydrates (R.6H₂O)).

The term “tautomers” or “tautomeric” refers to two or moreinterconvertible compounds resulting from at least one formal migrationof a hydrogen atom and at least one change in valency (e.g., a singlebond to a double bond, a triple bond to a single bond, or vice versa).The exact ratio of the tautomers depends on several factors, includingtemperature, solvent, and pH. Tautomerizations (i.e., the reactionproviding a tautomeric pair) may catalyzed by acid or base. Exemplarytautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim,enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.

It is also to be understood that compounds that have the same molecularformula but differ in the nature or sequence of bonding of their atomsor the arrangement of their atoms in space are termed “isomers”. Isomersthat differ in the arrangement of their atoms in space are termed“stereoisomers”.

Stereoisomers that are not mirror images of one another are termed“diastereomers” and those that are non-superimposable mirror images ofeach other are termed “enantiomers”. When a compound has an asymmetriccenter, for example, it is bonded to four different groups, a pair ofenantiomers is possible. An enantiomer can be characterized by theabsolute configuration of its asymmetric center and is described by theR- and S-sequencing rules of Cahn and Prelog, or by the manner in whichthe molecule rotates the plane of polarized light and designated asdextrorotatory or levorotatory (i.e., as (+) or (−)-isomersrespectively). A chiral compound can exist as either individualenantiomer or as a mixture thereof. A mixture containing equalproportions of the enantiomers is called a “racemic mixture”.

The term “polymorphs” refers to a crystalline form of a compound (or asalt, hydrate, or solvate thereof) in a particular crystal packingarrangement. All polymorphs have the same elemental composition.Different crystalline forms usually have different X-ray diffractionpatterns, infrared spectra, melting points, density, hardness, crystalshape, optical and electrical properties, stability, and solubility.Recrystallization solvent, rate of crystallization, storage temperature,and other factors may cause one crystal form to dominate. Variouspolymorphs of a compound can be prepared by crystallization underdifferent conditions.

The term “co-crystal” refers to a crystalline structure composed of atleast two components. In certain embodiments, a co-crystal may contain acompound of the present invention and one or more other component,including but not limited to, atoms, ions, molecules, or solventmolecules. In certain embodiments, a co-crystal may contain a compoundof the present invention and one or more components related to saidcompound, including not limited to, an isomer, tautomer, salt, solvate,hydrate, synthetic precursor, synthetic derivative, fragment or impurityof said compound. Co-crystals may be useful to improve the properties(e.g., solubility, stability, and ease of formulation) of a compound ofthe present invention.

The term “isotopes” refers to variants of a particular chemical elementsuch that, while all isotopes of a given element share the same numberof protons in each atom of the element, those isotopes differ in thenumber of neutrons. The term “radioactivity” or “radioactive decay”refers to the process by which a nucleus of an unstable isotope (e.g.,¹⁸F) loses energy by emitting particles or rays (e.g., alpha particles,beta particles, and gamma rays) of electromagnetic radiation. Such anunstable isotope or a material including the unstable isotope isreferred to as “radioactive.” The Curie (Ci) is a non-SI(non-International System of Units) unit of radioactivity and is definedas 1 Ci=3.7×10¹⁰ decays per second. The term “specific activity” refersto the unit radioactivity of a material (e.g., any compound disclosedherein, or a salt, tautomer, stereoisomer, or isotopically labeledderivative (e.g., ¹⁸F-labeled derivative) thereof). In certainembodiments, the term “specific activity” refers to the radioactivity ofa material per micromole (μmol) of the material.

The term “isotopically labeled derivative” or “isotopically labeled”refers to a compound wherein one or more atoms in the compound (or in anassociated ion or molecule of a salt, hydrate, or solvate) has beenreplaced with an isotope of the same element. For the given element orposition in the molecule the isotope will be enriched, or present in ahigher percentage of all atoms of the element or of all atoms at theposition in the molecule in a sample, relative to an unlabeled variant.In certain embodiments, the enriched isotope will be a stable isotope.In certain embodiments, the enriched isotope will be an unstable orradioactive isotope (e.g., a radionuclide). In certain embodiments, theenriched isotope may be detected by a measurement technique, includingbut not limited to nuclear magnetic resonance, mass spectrometry,infrared spectroscopy, or a technique that measures radioactive decay.

The term “prodrugs” refers to compounds that have cleavable groups andbecome by solvolysis or under physiological conditions the compoundsdescribed herein, which are pharmaceutically active in vivo. Suchexamples include, but are not limited to, choline ester derivatives andthe like, N-alkylmorpholine esters and the like. Other derivatives ofthe compounds described herein have activity in both their acid and acidderivative forms, but in the acid sensitive form often offer advantagesof solubility, tissue compatibility, or delayed release in the mammalianorganism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24,Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well knownto practitioners of the art, such as, for example, esters prepared byreaction of the parent acid with a suitable alcohol, or amides preparedby reaction of the parent acid compound with a substituted orunsubstituted amine, or acid anhydrides, or mixed anhydrides. Simplealiphatic or aromatic esters, amides, and anhydrides derived from acidicgroups pendant on the compounds described herein are particularprodrugs. In some cases it is desirable to prepare double ester typeprodrugs such as (acyloxy)alkyl esters or((alkoxycarbonyl)oxy)alkylesters. C₁-C₈ alkyl, C₂-C₈ alkenyl, C₂-C₈alkynyl, aryl, C₇-C₁₂ substituted aryl, and C₇-C₁₂ arylalkyl esters ofthe compounds described herein may be preferred.

The term “inhibition”, “inhibiting”, “inhibit,” or “inhibitor” refer tothe ability of a compound to reduce, slow, halt or prevent activity of aparticular biological process (e.g., activity of a bromodomain and/or abromodomain-containing protein) in a cell relative to vehicle.

As used herein the term “inhibit” or “inhibition” in the context ofenzymes, for example, in the context of CDK (e.g., CDK7, CDK12, CDK13),refers to a reduction in the activity of the enzyme. In someembodiments, the term refers to a reduction in the level of enzymeactivity, e.g., CDK (e.g., CDK7, CDK12, CDK13) activity, to a level thatis statistically significantly lower than an initial level, which may,for example, be a baseline level of enzyme activity. In someembodiments, the term refers to a reduction in the level of enzymeactivity, e.g., CDK (e.g., CDK7, CDK12, CDK13) activity, to a level thatis less than 75%, less than 50%, less than 40%, less than 30%, less than25%, less than 20%, less than 10%, less than 9%, less than 8%, less than7%, less than 6%, less than 5%, less than 4%, less than 3%, less than2%, less than 1%, less than 0.5%, less than 0.1%, less than 0.01%, lessthan 0.001%, or less than 0.0001% of an initial level, which may, forexample, be a baseline level of enzyme activity.

When a compound, pharmaceutical composition, method, use, or kit isreferred to as “selectively,” “specifically,” or “competitively” bindinga first protein or a first chromatin, the compound, pharmaceuticalcomposition, method, use, or kit binds the first protein or the firstchromatin with a higher binding affinity (e.g., not less than about2-fold, not less than about 5-fold, not less than about 10-fold, notless than about 30-fold, not less than about 100-fold, not less thanabout 1,000-fold, or not less than about 10,000-fold) than binding asecond protein or second chromatin that is different from the firstprotein and the first chromatin. When a compound, pharmaceuticalcomposition, method, use, or kit is referred to as “selectively,”“specifically,” or “competitively” modulating (e.g., increasing orinhibiting) the activity of a bromodomain-containing protein, thecompound, pharmaceutical composition, method, use, or kit modulates theactivity of the bromodomain-containing protein to a greater extent(e.g., not less than about 2-fold, not less than about 5-fold, not lessthan about 10-fold, not less than about 30-fold, not less than about100-fold, not less than about 1,000-fold, or not less than about10,000-fold) than the activity of at least one protein that is differentfrom the bromodomain-containing protein.

The term “aberrant activity” refers to activity deviating from normalactivity, that is, abnormal activity. The term “increased activity”refers to activity higher than normal activity.

The terms “composition” and “formulation” are used interchangeably.

A “subject” to which administration is contemplated refers to a human(i.e., male or female of any age group, e.g., pediatric subject (e.g.,infant, child, or adolescent) or adult subject (e.g., young adult,middle-aged adult, or senior adult)) or non-human animal. In certainembodiments, the non-human animal is a mammal (e.g., primate (e.g.,cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g.,cattle, pig, horse, sheep, goat, cat, or dog), or bird (e.g.,commercially relevant bird, such as chicken, duck, goose, or turkey)).In certain embodiments, the non-human animal is a fish, reptile, oramphibian. The non-human animal may be a male or female at any stage ofdevelopment. The non-human animal may be a transgenic animal orgenetically engineered animal. A “patient” refers to a human subject inneed of treatment of a disease.

The term “biological sample” refers to any sample including tissuesamples (such as tissue sections and needle biopsies of a tissue); cellsamples (e.g., cytological smears (such as Pap or blood smears) orsamples of cells obtained by microdissection); samples of wholeorganisms (such as samples of yeasts or bacteria); or cell fractions,fragments or organelles (such as obtained by lysing cells and separatingthe components thereof by centrifugation or otherwise). Other examplesof biological samples include blood, serum, urine, semen, fecal matter,cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus,biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy),nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccalswabs), or any material containing biomolecules that is derived fromanother biological sample.

The terms “administer,” “administering,” or “administration” refers toimplanting, absorbing, ingesting, injecting, inhaling, or otherwiseintroducing a compound described herein, or a composition thereof, into,in, or on a subject.

The terms “treatment,” “treat,” and “treating” refer to reversing,alleviating, delaying the onset of, or inhibiting the progress of adisease described herein. In some embodiments, treatment may beadministered after one or more signs or symptoms of the disease havedeveloped or have been observed. In other embodiments, treatment may beadministered in the absence of signs or symptoms of the disease. Forexample, treatment may be administered to a susceptible subject prior tothe onset of symptoms (e.g., in light of a history of symptoms and/or inlight of exposure to a pathogen). Treatment may also be continued aftersymptoms have resolved, for example, to delay or prevent recurrence.

The term “prevent,” “preventing,” or “prevention” refers to aprophylactic treatment of a subject who has not and had not beendiagnosed with a disease but is at risk of developing the disease. Theterm “prevent,” “preventing,” or “prevention” also refers to aprophylactic treatment of a subject who was suffering from a disease orhas not been diagnosed with the disease, but is at risk of regression orrecurrence of the disease. In certain embodiments, the subject is at ahigher risk of developing the disease or at a higher risk of regressionof the disease than an average healthy member of a population.

The terms “condition,” “disease,” and “disorder” are usedinterchangeably.

An “effective amount” of a compound described herein refers to an amountsufficient to elicit the desired biological response, i.e., treating thecondition. As will be appreciated by those of ordinary skill in thisart, the effective amount of a compound described herein may varydepending on such factors as the desired biological endpoint, thepharmacokinetics of the compound, the condition being treated, the modeof administration, and the age and health of the subject. In certainembodiments, an effective amount is a therapeutically effective amount.In certain embodiments, an effective amount is a prophylactic treatment.In certain embodiments, an effective amount is the amount of a compounddescribed herein in a single dose. In certain embodiments, an effectiveamount is the combined amounts of a compound described herein inmultiple doses.

A “therapeutically effective amount” of a compound described herein isan amount sufficient to provide a therapeutic benefit in the treatmentof a condition or to delay or minimize one or more symptoms associatedwith the condition. A therapeutically effective amount of a compoundmeans an amount of therapeutic agent, alone or in combination with othertherapies, which provides a therapeutic benefit in the treatment of thecondition. The term “therapeutically effective amount” can encompass anamount that improves overall therapy, reduces or avoids symptoms, signs,or causes of the condition, and/or enhances the therapeutic efficacy ofanother therapeutic agent. In certain embodiments, a therapeuticallyeffective amount is an amount sufficient for inhibiting CDK (e.g., CDK7,CDK12, CDK13). In certain embodiments, a therapeutically effectiveamount is an amount sufficient for treating an acute inflammatorydisease (e.g., rheumatoid arthritis, Crohn's disease, or fibrosis)and/or a proliferative disease (e.g., cancer, benign neoplasm, diseasesassociated with angiogenesis, inflammatory diseases, autoinflammatorydiseases, autoimmune diseases, pancreatic cancer, lung cancer (e.g.small cell lung cancer (SCLC), non-small cell lung cancer), prostatecancer, breast cancer, ovarian cancer, kidney cancer, liver cancer,Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, andcolorectal cancer). In certain embodiments, a therapeutically effectiveamount is an amount sufficient for inhibiting CDK (e.g., CDK7, CDK12,CDK13) and for treating an acute inflammatory disease (e.g., rheumatoidarthritis, Crohn's disease, or fibrosis) and/or a proliferative disease(e.g., cancer, benign neoplasm, diseases associated with angiogenesis,inflammatory diseases, autoinflammatory diseases, autoimmune diseases,pancreatic cancer, lung cancer (e.g. small cell lung cancer (SCLC), andnon-small cell lung cancer), prostate cancer, breast cancer, ovariancancer, kidney cancer, liver cancer, Ewing's sarcoma, osteosarcoma,brain cancer, neuroblastoma, and colorectal cancer).

A “prophylactically effective amount” of a compound described herein isan amount sufficient to prevent a condition, or one or more symptomsassociated with the condition or prevent its recurrence. Aprophylactically effective amount of a compound means an amount of atherapeutic agent, alone or in combination with other agents, whichprovides a prophylactic benefit in the prevention of the condition. Theterm “prophylactically effective amount” can encompass an amount thatimproves overall prophylaxis or enhances the prophylactic efficacy ofanother prophylactic agent. In certain embodiments, a prophylacticallyeffective amount is an amount sufficient for inhibiting CDK (e.g., CDK7,CDK12, CDK13). In certain embodiments, a prophylactically effectiveamount is an amount sufficient for treating an acute inflammatorydisease (e.g., rheumatoid arthritis, Crohn's disease, or fibrosis)and/or a proliferative disease (e.g., cancer, benign neoplasm, diseasesassociated with angiogenesis, inflammatory diseases, autoinflammatorydiseases, autoimmune diseases, pancreatic cancer, lung cancer (e.g.small cell lung cancer (SCLC), and non-small cell lung cancer), prostatecancer, breast cancer, ovarian cancer, kidney cancer, liver cancer,Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, andcolorectal cancer). In certain embodiments, a prophylactically effectiveamount is an amount sufficient for inhibiting CDK (e.g., CDK7, CDK12,CDK13) and for treating acute inflammatory disease (e.g., rheumatoidarthritis, Crohn's disease, or fibrosis) and/or a proliferative disease(e.g., cancer, benign neoplasm, diseases associated with angiogenesis,inflammatory diseases, autoinflammatory diseases, autoimmune diseases,pancreatic cancer, lung cancer (e.g. small cell lung cancer (SCLC), andnon-small cell lung cancer), prostate cancer, breast cancer, ovariancancer, kidney cancer, liver cancer, Ewing's sarcoma, osteosarcoma,brain cancer, neuroblastoma, and colorectal cancer).

A “proliferative disease” refers to a disease that occurs due toabnormal growth or extension by the multiplication of cells (Walker,Cambridge Dictionary of Biology; Cambridge University Press: Cambridge,UK, 1990). A proliferative disease may be associated with: 1) thepathological proliferation of normally quiescent cells; 2) thepathological migration of cells from their normal location (e.g.,metastasis of neoplastic cells); 3) the pathological expression ofproteolytic enzymes such as the matrix metalloproteinases (e.g.,collagenases, gelatinases, and elastases); or 4) the pathologicalangiogenesis as in proliferative retinopathy and tumor metastasis.Exemplary proliferative diseases include cancers (i.e., “malignantneoplasms”), benign neoplasms, diseases associated with angiogenesis,inflammatory diseases, and autoimmune diseases.

The term “angiogenesis” refers to the physiological process throughwhich new blood vessels form from pre-existing vessels. Angiogenesis isdistinct from vasculogenesis, which is the de novo formation ofendothelial cells from mesoderm cell precursors. The first vessels in adeveloping embryo form through vasculogenesis, after which angiogenesisis responsible for most blood vessel growth during normal or abnormaldevelopment. Angiogenesis is a vital process in growth and development,as well as in wound healing and in the formation of granulation tissue.However, angiogenesis is also a fundamental step in the transition oftumors from a benign state to a malignant one, leading to the use ofangiogenesis inhibitors in the treatment of cancer. Angiogenesis may bechemically stimulated by angiogenic proteins, such as growth factors(e.g., VEGF). “Pathological angiogenesis” refers to abnormal (e.g.,excessive or insufficient) angiogenesis that amounts to and/or isassociated with a disease.

The terms “neoplasm” and “tumor” are used herein interchangeably andrefer to an abnormal mass of tissue wherein the growth of the masssurpasses and is not coordinated as in the growth of normal tissue. Aneoplasm or tumor may be “benign” or “malignant,” depending on thefollowing characteristics: degree of cellular differentiation (includingmorphology and functionality), rate of growth, local invasion, andmetastasis. A “benign neoplasm” is generally well differentiated, hascharacteristically slower growth than a malignant neoplasm, and remainslocalized to the site of origin. In addition, a benign neoplasm does nothave the capacity to infiltrate, invade, or metastasize to distantsites. Exemplary benign neoplasms include, but are not limited to,lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheickeratoses, lentigos, and sebaceous hyperplasias. In some cases, certain“benign” tumors may later give rise to malignant neoplasms, which mayresult from additional genetic changes in a subpopulation of the tumor'sneoplastic cells, and these tumors are referred to as “pre-malignantneoplasms.” An exemplary pre-malignant neoplasm is a teratoma. Incontrast, a “malignant neoplasm” is generally poorly differentiated(anaplasia) and has characteristically rapid growth accompanied byprogressive infiltration, invasion, and destruction of the surroundingtissue. Furthermore, a malignant neoplasm generally has the capacity tometastasize to distant sites. The term “metastasis,” “metastatic,” or“metastasize” refers to the spread or migration of cancerous cells froma primary or original tumor to another organ or tissue and is typicallyidentifiable by the presence of a “secondary tumor” or “secondary cellmass” of the tissue type of the primary or original tumor and not ofthat of the organ or tissue in which the secondary (metastatic) tumor islocated. For example, a prostate cancer that has migrated to bone issaid to be metastasized prostate cancer and includes cancerous prostatecancer cells growing in bone tissue.

The term “cancer” refers to a class of diseases characterized by thedevelopment of abnormal cells that proliferate uncontrollably and havethe ability to infiltrate and destroy normal body tissues. See, e.g.,Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins:Philadelphia, 1990. Exemplary cancers include, but are not limited to,hematological malignancies. Additional exemplary cancers include, butare not limited to, acoustic neuroma; adenocarcinoma; adrenal glandcancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma,lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benignmonoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma);bladder cancer; breast cancer (e.g., adenocarcinoma of the breast,papillary carcinoma of the breast, mammary cancer, medullary carcinomaof the breast, triple negative breast cancer (TNBC)); brain cancer(e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma,oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor;cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma;chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer,rectal cancer, colorectal adenocarcinoma); connective tissue cancer;epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi'ssarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer(e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g.,adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing'ssarcoma; ocular cancer (e.g., intraocular melanoma, retinoblastoma);familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g.,stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germcell cancer; head and neck cancer (e.g., head and neck squamous cellcarcinoma, oral cancer (e.g., oral squamous cell carcinoma), throatcancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngealcancer, oropharyngeal cancer)); heavy chain disease (e.g., alpha chaindisease, gamma chain disease, mu chain disease; hemangioblastoma;hypopharynx cancer; inflammatory myofibroblastic tumors; immunocyticamyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor,renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC),malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, smallcell lung cancer (SCLC), non-small cell lung cancer (NSCLC),adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g.,systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS);mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera(PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM)a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronicmyelocytic leukemia (CML), chronic neutrophilic leukemia (CNL),hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g.,neurofibromatosis (NF) type 1 or type 2, schwannomatosis);neuroendocrine cancer (e.g., gastroenteropancreatic neuroendocrine tumor(GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovariancancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarianadenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g.,pancreatic adenocarcinoma, intraductal papillary mucinous neoplasm(IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of thepenis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT);plasma cell neoplasia; paraneoplastic syndromes; intraepithelialneoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectalcancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g.,squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basalcell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); softtissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma,malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma,fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestinecancer; sweat gland carcinoma; synovioma; testicular cancer (e.g.,seminoma, testicular embryonal carcinoma); thyroid cancer (e.g.,papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC),medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvarcancer (e.g., Paget's disease of the vulva).

The term “hematological malignancy” refers to tumors that affect blood,bone marrow, and/or lymph nodes. Exemplary hematological malignanciesinclude, but are not limited to, leukemia, such as acute lymphoblasticleukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia(AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML)(e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL)(e.g., B-cell CLL, T-cell CLL)); lymphoma, such as Hodgkin lymphoma (HL)(e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g.,B-cell NHL, such as diffuse large cell lymphoma (DLCL) (e.g., diffuselarge B-cell lymphoma (DLBCL, e.g., activated B-cell (ABC) DLBCL(ABC-DLBCL))), follicular lymphoma, chronic lymphocytic leukemia/smalllymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginalzone B-cell lymphoma (e.g., mucosa-associated lymphoid tissue (MALT)lymphoma, nodal marginal zone B-cell lymphoma, splenic marginal zoneB-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt'slymphoma, Waldenström's macroglobulinemia (WM, lymphoplasmacyticlymphoma), hairy cell leukemia (HCL), immunoblastic large cell lymphoma,precursor B-lymphoblastic lymphoma, central nervous system (CNS)lymphoma (e.g., primary CNS lymphoma and secondary CNS lymphoma); andT-cell NHL, such as precursor T-lymphoblastic lymphoma/leukemia,peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma(CTCL) (e.g., mycosis fungoides, Sezary syndrome), angioimmunoblasticT-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathytype T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma,and anaplastic large cell lymphoma); lymphoma of an immune privilegedsite (e.g., cerebral lymphoma, ocular lymphoma, lymphoma of theplacenta, lymphoma of the fetus, testicular lymphoma); a mixture of oneor more leukemia/lymphoma as described above; myelodysplasia; andmultiple myeloma (MM).

The term “inflammatory disease” refers to a disease caused by, resultingfrom, or resulting in inflammation. The term “inflammatory disease” mayalso refer to a dysregulated inflammatory reaction that causes anexaggerated response by macrophages, granulocytes, and/or T-lymphocytesleading to abnormal tissue damage and/or cell death. An inflammatorydisease can be either an acute or chronic inflammatory condition and canresult from infections or non-infectious causes Inflammatory diseasesinclude, without limitation, atherosclerosis, arteriosclerosis,autoimmune disorders, multiple sclerosis, systemic lupus erythematosus,polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis,tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis,rheumatoid arthritis, inflammatory arthritis, Sjogren's syndrome, giantcell arteritis, progressive systemic sclerosis (scleroderma), ankylosingspondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid,diabetes (e.g., Type I), myasthenia gravis, Hashimoto's thyroiditis,Graves' disease, Goodpasture's disease, mixed connective tissue disease,sclerosing cholangitis, inflammatory bowel disease, Crohn's disease,ulcerative colitis, pernicious anemia, inflammatory dermatoses, usualinterstitial pneumonitis (UIP), asbestosis, silicosis, bronchiectasis,berylliosis, talcosis, pneumoconiosis, sarcoidosis, desquamativeinterstitial pneumonia, lymphoid interstitial pneumonia, giant cellinterstitial pneumonia, cellular interstitial pneumonia, extrinsicallergic alveolitis, Wegener's granulomatosis and related forms ofangiitis (temporal arteritis and polyarteritis nodosa), inflammatorydermatoses, hepatitis, delayed-type hypersensitivity reactions (e.g.,poison ivy dermatitis), pneumonia, respiratory tract inflammation, AdultRespiratory Distress Syndrome (ARDS), encephalitis, immediatehypersensitivity reactions, asthma, hay fever, allergies, acuteanaphylaxis, rheumatic fever, glomerulonephritis, pyelonephritis,cellulitis, cystitis, chronic cholecystitis, ischemia (ischemic injury),reperfusion injury, allograft rejection, host-versus-graft rejection,appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis,cervicitis, cholangitis, chorioamnionitis, conjunctivitis,dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis,enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis,gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis,myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis,osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis,pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis,salpingitis, sinusitis, stomatitis, synovitis, testitis, tonsillitis,urethritis, urocystitis, uveitis, vaginitis, vasculitis, vulvitis,vulvovaginitis, angitis, chronic bronchitis, osteomyelitis, opticneuritis, temporal arteritis, transverse myelitis, necrotizingfasciitis, and necrotizing enterocolitis.

An “autoimmune disease” refers to a disease arising from aninappropriate immune response of the body of a subject againstsubstances and tissues normally present in the body. In other words, theimmune system mistakes some part of the body as a pathogen and attacksits own cells. This may be restricted to certain organs (e.g., inautoimmune thyroiditis) or involve a particular tissue in differentplaces (e.g., Goodpasture's disease which may affect the basementmembrane in both the lung and kidney). The treatment of autoimmunediseases is typically with immunosuppression, e.g., medications whichdecrease the immune response. Exemplary autoimmune diseases include, butare not limited to, glomerulonephritis, Goodpasture's syndrome,necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemiclupus erythematosis, rheumatoid arthritis, psoriatic arthritis, systemiclupus erythematosis, psoriasis, ulcerative colitis, systemic sclerosis,dermatomyositis/polymyositis, anti-phospholipid antibody syndrome,scleroderma, pemphigus vulgaris, ANCA-associated vasculitis (e.g.,Wegener's granulomatosis, microscopic polyangiitis), uveitis, Sjogren'ssyndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis,Lyme disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, andcardiomyopathy.

The term “kinase” is a type of enzyme that transfers phosphate groupsfrom high energy donor molecules, such as ATP, to specific substrates,referred to as phosphorylation. Kinases are part of the larger family ofphosphotransferases. One of the largest groups of kinases are proteinkinases, which act on and modify the activity of specific proteins.Kinases are used extensively to transmit signals and control complexprocesses in cells. Various other kinases act on small molecules such aslipids, carbohydrates, amino acids, and nucleotides, either forsignaling or to prime them for metabolic pathways. Kinases are oftennamed after their substrates. More than 500 different protein kinaseshave been identified in humans. Exemplary human protein kinases include,but are not limited to, AAK1, ABL, ACK, ACTR2, ACTR2B, AKT1, AKT2, AKT3,ALK, ALK1, ALK2, ALK4, ALK7, AMPKa1, AMPKa2, ANKRD3, ANPa, ANPb, ARAF,ARAFps, ARG, AurA, AurAps1, AurAps2, AurB, AurBps1, AurC, AXL, BARK1,BARK2, BIKE, BLK, BMPR1A, BMPR1Aps1, BMPR1Aps2, BMPR1B, BMPR2, BMX,BRAF, BRAFps, BRK, BRSK1, BRSK2, BTK, BUB1, BUBR1, CaMK1a, CaMK1b,CaMK1d, CaMK1g, CaMK2a, CaMK2b, CaMK2d, CaMK2g, CaMK4, CaMKK1, CaMKK2,caMLCK, CASK, CCK4, CCRK, CDC2, CDC7, CDK10, CDK11, CDK2, CDK3, CDK4,CDK4ps, CDK5, CDK5ps, CDK6, CDK7, CDK7ps, CDK8, CDK8ps, CDK9, CDKL1,CDKL2, CDKL3, CDKL4, CDKL5, CGDps, CHED, CHK1, CHK2, CHK2ps1, CHK2ps2,CK1a, CK1a2, CK1aps1, CK1aps2, CK1aps3, CK1d, CK1e, CK1g1, CK1g2,CK1g2ps, CK1g3, CK2a1, CK2a1-rs, CK2a2, CLIK1, CLIK1L, CLK1, CLK2,CLK2ps, CLK3, CLK3ps, CLK4, COT, CRIK, CRK7, CSK, CTK, CYGD, CYGF,DAPK1, DAPK2, DAPK3, DCAMKL1, DCAMKL2, DCAMKL3, DDR1, DDR2, DLK, DMPK1,DMPK2, DRAK1, DRAK2, DYRK1A, DYRK1B, DYRK2, DYRK3, DYRK4, EGFR, EphA1,EphA10, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphB1, EphB2,EphB3, EphB4, EphB6, Erk1, Erk2, Erk3, Erk3ps1, Erk3ps2, Erk3ps3,Erk3ps4, Erk4, Erk5, Erk7, FAK, FER, FERps, FES, FGFR1, FGFR2, FGFR3,FGFR4, FGR, FLT1, FLT1ps, FLT3, FLT4, FMS, FRK, Fused, FYN, GAK, GCK,GCN2, GCN22, GPRK4, GPRK5, GPRK6, GPRK6ps, GPRK7, GSK3A, GSK3B, Haspin,HCK, HER2/ErbB2, HER3/ErbB3, HER4/ErbB4, HH498, HIPK1, HIPK2, HIPK3,HIPK4, HPK1, HRI, HRIps, HSER, HUNK, ICK, IGF1R, IKKa, IKKb, IKKe, ILK,INSR, IRAK1, IRAK2, IRAK3, IRAK4, IRE1, IRE2, IRR, ITK, JAK1, JAK2,JAK3, JNK1, JNK2, JNK3, KDR, KHS1, KHS2, KIS, KIT, KSGCps, KSR1, KSR2,LATS1, LATS2, LCK, LIMK1, LIMK2, LIMK2ps, LKB1, LMR1, LMR2, LMR3, LOK,LRRK1, LRRK2, LTK, LYN, LZK, MAK, MAP2K1, MAP2K1ps, MAP2K2, MAP2K2ps,MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K2, MAP3K3, MAP3K4,MAP3K5, MAP3K6, MAP3K7, MAP3K8, MAPKAPK2, MAPKAPK3, MAPKAPK5,MAPKAPKps1, MARK1, MARK2, MARK5, MARK4, MARKps01, MARKps02, MARKps03,MARKps04, MARKps05, MARKps07, MARKps08, MARKps09, MARKps10, MARKps11,MARKps12, MARKps13, MARKps15, MARKps16, MARKps17, MARKps18, MARKps19,MARKps20, MARKps21, MARKps22, MARKps23, MARKps24, MARKps25, MARKps26,MARKps27, MARKps28, MARKps29, MARKps30, MAST1, MAST2, MAST3, MAST4,MASTL, MELK, MER, MET, MISR2, MLK1, MLK2, MLK3, MLK4, MLKL, MNK1,MNK1ps, MNK2, MOK, MOS, MPSK1, MPSK1ps, MRCKa, MRCKb, MRCKps, MSK1,MSK12, MSK2, MSK22, MSSK1, MST1, MST2, MST3, MST3ps, MST4, MUSK, MYO3A,MYO3B, MYT1, NDR1, NDR2, NEK1, NEK10, NEK11, NEK2, NEK2ps1, NEK2ps2,NEK2ps3, NEK3, NEK4, NEK4ps, NEK5, NEK6, NEK7, NEK8, NEK9, NIK, NIM1,NLK, NRBP1, NRBP2, NuaK1, NuaK2, Obscn, Obscn2, OSR1, p38a, p38b, p38d,p38g, p70S6K, p70S6Kb, p70S6Kps1, p70S6Kps2, PAK1, PAK2, PAK2ps, PAK3,PAK4, PAK5, PAK6, PASK, PBK, PCTAIRE1, PCTAIRE2, PCTAIRE3, PDGFRa,PDGFRb, PDK1, PEK, PFTAIRE1, PFTAIRE2, PHKg1, PHKg1ps1, PHKg1ps2,PHKg1ps3, PHKg2, PIK3R4, PIM1, PIM2, PIM3, PINK1, PITSLRE, PKACa, PKACb,PKACg, PKCa, PKCb, PKCd, PKCe, PKCg, PKCh, PKCi, PKCips, PKCt, PKCz,PKD1, PKD2, PKD3, PKG1, PKG2, PKN1, PKN2, PKN₃, PKR, PLK1, PLK1ps1,PLK1ps2, PLK2, PLK3, PLK4, PRKX, PRKXps, PRKY, PRP4, PRP4ps, PRPK,PSKH1, PSKH1ps, PSKH2, PYK2, QIK, QSK, RAF1, RAF1ps, RET, RHOK, RIPK1,RIPK2, RIPK3, RNAseL, ROCK1, ROCK2, RON, ROR1, ROR2, ROS, RSK1, RSK12,RSK2, RSK22, RSK3, RSK32, RSK4, RSK42, RSKL1, RSKL2, RYK, RYKps, SAKps,SBK, SCYL1, SCYL2, SCYL2ps, SCYL3, SGK, SgKO50ps, SgK069, SgK071,SgK085, SgK110, SgK196, SGK2, SgK223, SgK269, SgK288, SGK3, SgK307,SgK384ps, SgK396, SgK424, SgK493, SgK494, SgK495, SgK496, SIK(e.g.,SIK1, SIK2), skMLCK, SLK, S1ob, smMLCK, SNRK, SPEG, SPEG2, SRC, SRM,SRPK1, SRPK2, SRPK2ps, SSTK, STK33, STK33ps, STLK3, STLK5, STLK6,STLK6ps1, STLK6-rs, SuRTK106, SYK, TAK1, TAO1, TAO2, TAO3, TBCK, TBK1,TEC, TESK1, TESK2, TGFbR1, TGFbR2, TIE1, TIE2, TLK1, TLK1ps, TLK2,TLK2ps1, TLK2ps2, TNK1, Trad, Trb1, Trb2, Trb3, Trio, TRKA, TRKB, TRKC,TSSK1, TSSK2, TSSK3, TSSK4, TSSKps1, TSSKps2, TTBK1, TTBK2, TTK, TTN,TXK, TYK2, TYK22, TYRO3, TYRO3ps, ULK1, ULK2, ULK3, ULK4, VACAMKL, VRK1,VRK2, VRK3, VRK3ps, Wee1, Wee1B, Wee1Bps, Wee1ps1, Wee1ps2, Wnk1, Wnk2,Wnk3, Wnk4, YANK1, YANK2, YANKS, YES, YESps, YSK1, ZAK, ZAP70, ZC1/HGK,ZC2/TNIK, ZC3/MINK, and ZC4/NRK.

The term “SRC family kinase” refers to a family of non-receptor tyrosineprotein kinases that includes nine members: SRCA subfamily that includesc-SRC (proto-oncogene tyrosine-protein kinase SRC), YES (proto-oncogenetyrosine-protein kinase Yes), FYN (proto-oncogene tyrosine-proteinkinase FYN), and FGR (Gardner-Rasheed feline sarcoma viral (v-FGR)oncogene homolog); SRCB subfamily that includes LCK (lymphocyte-specificprotein tyrosine kinase), HCK (tyrosine-protein kinase HCK, hemopoieticcell kinase), BLK (tyrosine-protein kinase BLK), and LYN(tyrosine-protein kinase LYN); and FRK (Fyn-related kinase).

The term “CDK” refers to a cyclin-dependent kinase. A CDK binds a cyclin(e.g., Cyclin H), which is a regulatory protein. CDKs phosphorylatetheir substrates at serines and threonines. The consensus sequence forthe phosphorylation site in the amino acid sequence of a CDK substrateis [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine,P is proline, X is any amino acid, K is lysine, and R is arginine. CDKsinclude CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10,CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19 and CDK20.

CDK7, cyclin-dependent kinase 7, is a CDK, wherein the substrate isCyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1. CDK7 isalternatively referred to as CAK1, HCAK, MO15, STK1, CDKN7, and p39MO15.Non-limiting examples of the nucleotide and protein sequences for humanCDK7 are described in GenBank Accession Number NP_001790, incorporatedherein by reference. The amino acid sequence of this CDK7 is as follows:

MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

CDK12, cyclin-dependent kinase 12, is a CDK, wherein the substrate isCyclin K or Flavopiridol. CDK12 is alternatively referred to asCdc2-related kinase, CDC2-related protein kinase 7, Cell division cycle2-related protein kinase 7, Cell division protein kinase 12, CRK7, CRKR,CRKRS, cyclin-dependent kinase 12, or KIAA0904. Non-limiting examples ofthe nucleotide and protein sequences for human CDK12 are described inUniprot Number Q9NYV4, which is incorporated herein by reference. Theamino acid sequence of this CDK12 is as follows:

MPNSERHGGKKDGSGGASGTLQPSSGGGSSNSRERHRLVSKHKRHKSKHSKDMGLVTPEAASLGTVIKPLVEYDDISSDSDTFSDDMAFKLDRRENDERRGSDRSDRLHKHRHHQHRRSRDLLKAKQTEKEKSQEVSSKSGSMKDRISGSSKRSNEETDDYGKAQVAKSSSKESRSSKLHKEKTRKERELKSGHKDRSKSHRKRETPKSYKTVDSPKRRSRSPHRKWSDSSKQDDSPSGASYGQDYDLSPSRSHTSSNYDSYKKSPGSTSRRQSVSPPYKEPSAYQSSTRSPSPYSRRQRSVSPYSRRRSSSYERSGSYSGRSPSPYGRRRSSSPFLSKRSLSRSPLPSRKSMKSRSRSPAYSRHSSSHSKKKRSSSRSRHSSISPVRLPLNSSLGAELSRKKKERAAAAAAAKMDGKESKGSPVFLPRKENSSVEAKDSGLESKKLPRSVKLEKSAPDTELVNVTHLNTEVKNSSDTGKVKLDENSEKHLVKDLKAQGTRDSKPIALKEEIVTPKETETSEKETPPPLPTIASPPPPLPTTTPPPQTPPLPPLPPIPALPQQPPLPPSQPAFSQVPASSTSTLPPSTHSKTSAVSSQANSQPPVQVSVKTQVSVTAAIPHLKTSTLPPLPLPPLLPGDDDMDSPKETLPSKPVKKEKEQRTRHLLTDLPLPPELPGGDLSPPDSPEPKAITPPQQPYKKRPKICCPRYGERRQTESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQSGVVVEEPPPSKTSRKETTSGTSTEPVKNSSPAPPQPAPGKVESGAGDAIGLADITQQLNQSELAVLLNLLQSQTDLSIPQMAQLLNIHSNPEMQQQLEALNQSISALTEATSQQQDSETMAPEESLKEAPSAPVILPSAEQTTLEASSTPADMQNILAVLLSQLMKTQEPAGSLEENNSDKNSGPQGPRRTPTMPQEEAAACPPHILPPEKRPPEPPGPPPPPPPPPLVEGDLSSAPQELNPAVTAALLQLLSQPEAEPPGHLPHEHQALRPMEYSTRPRPNRTYGNTDGPETGFSAIDTDERNSGPALTESLVQTLVKNRTFSGSLSHLGESSSYQGTGSVQFPGDQDLRFARVPLALHPVVGQPFLKAEGSSNSVVHAETKLQNYGELGPGTTGASSSGAGLHWGGPTQSSAYGKLYRGPTRVPPRGGRGRGVPY

CDK13, cyclin-dependent kinase 13, is a CDK, wherein the relevant cyclinis cyclin K and a reference inhibitor is the pan-CDK inhibitorFlavopiridol and the c-terminal domain (CTD) of RNA-polymerase II is aphysiological substrate. CDK13 is alternatively referred to as CHED;CDC2L; CDC2L5; or hCDK13. Non-limiting examples of the nucleotide andprotein sequences for human CDK12 are described in GenBank AccessionNumber M80629, which is incorporated herein by reference. The amino acidsequence of this CDK13 is as follows:

MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQPPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVKRLARGKRRAGGRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVSSQSEQGLLLGGASAATAATAAGGTGGSGGSPASSSGTQRRGEGSERRPRRDRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRHSHSGEERAEVAKSGSSSSSGGRRKSASATSSSSSSRKDRDSKAHRSRTKSSKEPPSAYKEPPKAYREDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSPYSRRLPRSPSPYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYSPVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLAAELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTKPPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPEDKEADSLRGNISVKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDIIGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLGLDDSRTNTPQGVLPSSQLKSQGSSNVAPVKTGPGQHLNHSELAILLNLLQSKTSVNMADFVQVLNIKVNSETQQQLNKINLPAGILATGEKQTDPSTPQQESSKPLGGIQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDVLLEERENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMRILELTPEPDRPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAALLQLLAQHQPQDDPKREGGIDYQAGDTYVSTSDYKDNFGSSSFSSAPYVSNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSESFPSSVAGYGDIYLNAGPMLFSGDKDHRFEYSHGPIAVLANSSDPSTGPESTHPLPAKMHNYNYGGNLQENPSGPSLMHGQTWTSPAQGPGYSQGYRGHIST STGRGRGRGLPY

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Cyclin dependent kinases (CDKs) are key regulators of the cell cycle.Their successive activation and inactivation drives the cycle forward.The activity of CDKs is regulated by multiple mechanisms such aspositive and negative phosphorylation, binding of regulatory proteinslike cyclins, and CDK inhibitors. CDK7 plays a critical role in theregulation of RNA polymerase II-mediated transcription ofprotein-encoding genes. Disruption of CDK7, CDK12, and/or CDK13signaling cause defects in transcription. However, a completeunderstanding of how these disruptions affect global transcription islacking. Furthermore, the absence of selective inhibitors of CDK7,CDK12, and CDK13 has hindered investigation of the transcriptional andfunctional consequences of acute and long-term inhibition of thesekinases under normal and pathological conditions. The present inventionprovides selective CDK7, CDK12, and/or CDK13 inhibitors and analogs,which have the ability to covalently modify a cysteine residue locatedoutside of the canonical kinase domain (i.e., Cys312 of CDK7, Cys1039 ofCDK12, and Cys1017 of CDK13). Selective covalent inhibitors of thesekinases may be useful in the treatment of various proliferative diseasesincluding cancer.

The present invention provides compounds, which inhibit the activity ofa kinase, for the prevention and/or treatment of a subject with aproliferative disease. In certain embodiments, the inventive compoundsinhibit the activity of cyclin-dependent kinase (CDK). In certainembodiments, the inventive compounds inhibit the activity of acyclin-dependent kinase 7 (CDK7). In certain embodiments, the inventivecompounds inhibit the activity of a cyclin-dependent kinase 12 (CDK12).In certain embodiments, the inventive compounds inhibit the activity ofa cyclin-dependent kinase 13 (CDK13). The present invention alsoprovides methods of using the compounds described herein, e.g., asbiological probes to study the inhibition of the activity of a kinase(e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)), and as therapeutics, e.g.,in the prevention and/or treatment of diseases associated with theoverexpression and/or aberrant activity of a kinase (e.g., CDK (e.g.CDK7, CDK12, and/or CDK13)). In certain embodiments, the diseases areproliferative diseases. The proliferative diseases that may be treatedand/or prevented include, but are not limited to, cancers (e.g., breastcancer, leukemia, melanoma, multiple myeloma), benign neoplasms,diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases. Also provided by thepresent disclosure are pharmaceutical compositions, kits, methods, anduses including a compound of Formula (I) as described herein.

Compounds

Aspects of the present disclosure relate to the compounds describedherein. The compounds described herein are purine, pyrazolo-triazine,and pyrazolo-pyrimidine containing compounds that are useful in treatingand/or preventing proliferative diseases in a subject, inhibiting theactivity of a protein kinase (e.g., CDK) in a subject or biologicalsample, and inducing apoptosis of a cell. In certain embodiments, acompound described herein is a compound of any one of Formulae(I)-(III), or a pharmaceutically acceptable salt, solvate, hydrate,polymorph, co-crystal, tautomer, stereoisomer, isotopically labeledderivative, or prodrug thereof. In certain embodiments, a compounddescribed herein is a compound of Formula (I), or a pharmaceuticallyacceptable salt thereof. In certain embodiments, a compound describedherein is a compound of Formula (II), or a pharmaceutically acceptablesalt thereof. In certain embodiments, a compound described herein is acompound of Formula (III), or a pharmaceutically acceptable saltthereof.

In certain embodiments, a compound described herein is of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein:

R¹ is optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted aryl, optionally substituted heterocyclyl,optionally substituted heteroaryl, —NR^(a)R^(b), —OR^(b), —SR^(b),—C(═O)R^(b), —C(═O)OR^(b), or —C(═O)NR^(a)R^(b), wherein each instanceof R^(a) and R^(b) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group whenattached to nitrogen, or an oxygen protecting group when attached tooxygen, or a sulfur protecting group when attached to sulfur; or R^(a)and R^(b) are joined to form an optionally substituted heterocyclic oroptionally substituted heteroaryl ring;

R³ is hydrogen, halogen, or optionally substituted C₁-C₆ alkyl;

R⁵ is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group;

L¹ is a bond, —NR^(L1)—(CH₂)_(t)—, —O—, or —S—;

R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group;

t is 0 or an integer between 1 and 5, inclusive;

Ring A is optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl;

L² is a bond, optionally substituted C₁₋₄ alkylene, —C(═O)—, —NR^(L2)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group;

Ring B is absent, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl; and

R² is any of Formulae (i-1)-(i-41):

wherein:

L³ is a bond or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain areindependently replaced with —C═O—, —O—, —S—, —NR^(3a)—, —NR^(L3a)C(═O)—,—C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—,—NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(L3b) groups are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring;

L⁴ is a bond or an optionally substituted, branched or unbranched C₁₋₆hydrocarbon chain;

each of R^(E1), R^(E2), and R^(E3) is independently hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CN, —CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE),—OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, and —SR^(EE), wherein eachoccurrence of R^(EE) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkoxy, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(EE) groups are joined toform an optionally substituted heterocyclic ring; or R^(E1) and R^(E3),or R^(E2) and R^(E3), or R^(E1) and R^(E2) are joined to form anoptionally substituted carbocyclic or optionally substitutedheterocyclic ring;

R^(E4) is a leaving group;

R^(E5) is halogen;

R^(E6) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or anitrogen protecting group;

each instance of Y is independently O, S, or NR^(E7), wherein R^(E7) ishydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group;

-   -   a is 1 or 2; and    -   each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as        valency permits; and    -   provided that the compound is not

In certain embodiments, a compound described herein is of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

R¹ is optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted aryl, optionally substituted heterocyclyl,optionally substituted heteroaryl, —NR^(a)R^(b), —OR^(b), —SR^(b),—C(═O)R^(b), —C(═O)OR^(b), or —C(═O)NR^(a)R^(b), wherein each instanceof R^(a) and R^(b) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group whenattached to nitrogen, or an oxygen protecting group when attached tooxygen, or a sulfur protecting group when attached to sulfur; or R^(a)and R^(b) are joined to form an optionally substituted heterocyclic oroptionally substituted heteroaryl ring;

each of R³ and R⁴ is independently hydrogen, halogen, or optionallysubstituted C₁-C₆ alkyl;

L¹ is a bond, —NR^(L1)—(CH₂)_(t)—, —O—, or —S—;

R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group;

t is 0 or an integer between 1 and 5, inclusive;

Ring A is optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl;

L² is a bond, optionally substituted C₁₋₄ alkylene, —C(═O)—, —NR^(L2)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group;

Ring B is absent, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl; and

R² is any of Formulae (i-1)-(i-41):

wherein:

L³ is a bond or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain areindependently replaced with —C═O—, —O—, —S—, —NR^(3a)—, —NR^(L3a)C(═O)—,—C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—,—NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(L3b) groups are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring;

L⁴ is a bond or an optionally substituted, branched or unbranched C₁₋₆hydrocarbon chain;

each of R^(E1), R^(E2), and R^(E3) is independently hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CN, —CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE),—OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, and —SR^(EE), wherein eachoccurrence of R^(EE) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkoxy, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(EE) groups are joined toform an optionally substituted heterocyclic ring;

or R^(E1) and R^(E3), or R^(E2) and R^(E3), or R^(E1) and R^(E2) arejoined to form an optionally substituted carbocyclic or optionallysubstituted heterocyclic ring;

R^(E4) is a leaving group;

R^(E5) is halogen;

R^(E6) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or anitrogen protecting group;

each instance of Y is independently O, S, or NR^(E7), wherein R^(E7) ishydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group;

a is 1 or 2; and

each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valencypermits.

In certain embodiments, a compound described herein is of Formula (III):

or a pharmaceutically acceptable salt thereof, wherein:

R¹ is optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted aryl, optionally substituted heterocyclyl,optionally substituted heteroaryl, —NR^(a)R^(b), —OR^(b), —SR^(b),—C(═O)R^(b), —C(═O)OR^(b), or —C(═O)NR^(a)R^(b), wherein each instanceof R^(a) and R^(b) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group whenattached to nitrogen, or an oxygen protecting group when attached tooxygen, or a sulfur protecting group when attached to sulfur; or R^(a)and R^(b) are joined to form an optionally substituted heterocyclic oroptionally substituted heteroaryl ring;

each of R³ and R⁴ is independently hydrogen, halogen, or optionallysubstituted C₁-C₆ alkyl;

L¹ is a bond, —NR^(L1)—(CH₂)_(t)—, —O—, or —S—;

R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group;

t is 0 or an integer between 1 and 5, inclusive;

Ring A is optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl;

L² is a bond, optionally substituted C₁₋₄ alkylene, —C(═O)—, —NR^(L2)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group;

Ring B is absent, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl; and

R² is any of Formulae (i-1)-(i-41):

wherein:

L³ is a bond or an optionally substituted C₁₋₄ hydrocarbon chain,optionally wherein one or more carbon units of the hydrocarbon chain areindependently replaced with —C═O—, —O—, —S—, —NR^(L3a)—,—NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(L3b) groups are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring;

L⁴ is a bond or an optionally substituted, branched or unbranched C₁₋₆hydrocarbon chain;

each of R^(E1), R^(E2), and R^(E3) is independently hydrogen, halogen,optionally substituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, optionallysubstituted heteroaryl, —CN, —CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE),—OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, and —SR^(EE), wherein eachoccurrence of R^(EE) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkoxy, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(EE) groups are joined toform an optionally substituted heterocyclic ring;

or R^(E1) and R^(E3), or R^(E2) and R^(E3), or R^(E1) and R^(E2) arejoined to form an optionally substituted carbocyclic or optionallysubstituted heterocyclic ring;

R^(E4) is a leaving group;

R^(E5) is halogen;

R^(E6) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or anitrogen protecting group;

each instance of Y is independently O, S, or NR^(E7), wherein R^(E7) ishydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group;

a is 1 or 2; and

each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valencypermits.

As generally defined herein in Formulae (I)-(III), R¹ is optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted aryl, optionally substituted heterocyclyl, optionallysubstituted heteroaryl, —NR^(a)R^(b), —OR^(b), —SR^(b), —C(═O)R^(b),—C(═O)OR^(b), or —C(═O)NR^(a)R^(b), wherein each instance of R^(a) andR^(b) is independently hydrogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group whenattached to nitrogen, or an oxygen protecting group when attached tooxygen, or a sulfur protecting group when attached to sulfur; or R^(a)and R^(b) are joined to form an optionally substituted heterocyclic oroptionally substituted heteroaryl ring.

In certain embodiments, R¹ is optionally substituted alkyl. In certainembodiments, R¹ is unsubstituted alkyl. In certain embodiments, R¹ issubstituted alkyl. In certain embodiments, R¹ is substituted alkyl. Incertain embodiments, R¹ is optionally substituted carbocyclylalkyl,optionally substituted arylalkyl, optionally substitutedheterocyclylalkyl, or optionally substituted heteroarylalkyl. In certainembodiments, R¹ is optionally substituted heteroaryl. In certainembodiments, R¹ is optionally substituted monocyclic heteroaryl. Incertain embodiments, R¹ is optionally substituted 5-membered heteroaryl.In certain embodiments, R¹ is optionally substituted 6-memberedheteroaryl. In certain embodiments, R¹ is optionally substitutedheterocyclyl. In certain embodiments, R¹ is optionally substitutedmonocyclic heterocyclyl. In certain embodiments, R¹ is optionallysubstituted 5-membered heterocyclyl. In certain embodiments, R¹ isoptionally substituted 6-membered heterocyclyl. In certain embodiments,R¹ is —OR^(b), wherein R^(b) is as defined herein. In certainembodiments, R¹ is —OR^(b), wherein R^(b) is optionally substitutedalkyl, optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or an oxygen protecting group. Incertain embodiments, R¹ is —SR^(b), wherein R^(b) is as defined herein.In certain embodiments, R¹ is —SR^(b), wherein R^(b) is optionallysubstituted alkyl, optionally substituted carbocyclyl, optionallysubstituted aryl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, or a sulfurprotecting group. In certain embodiments, R¹ is —C(═O)R^(b), whereinR^(b) is as defined herein. In certain embodiments, R¹ is —C(═O)R^(b),wherein R^(b) is optionally substituted alkyl, optionally substitutedcarbocyclyl, optionally substituted aryl, optionally substitutedheterocyclyl, optionally substituted aryl, optionally substitutedheteroaryl. In certain embodiments, R¹ is —C(═O)OR^(b), wherein R^(b) isas defined herein. In certain embodiments, R¹ is —C(═O)OR^(b), whereinR^(b) is optionally substituted alkyl, optionally substitutedcarbocyclyl, optionally substituted aryl, optionally substitutedheterocyclyl, optionally substituted aryl, optionally substitutedheteroaryl, or an oxygen protecting group. In certain embodiments, R¹ isC(═O)NR^(a)R^(b), wherein R^(a) and R^(b) are as defined herein. Incertain embodiments, R¹ is C(═O)NR^(a)R^(b), wherein each instance ofR^(a) and R^(b) is independently optionally substituted alkyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group, orR^(a) and R^(b) are taken together with the nitrogen to form anoptionally substituted heterocyclyl ring. In certain embodiments, R¹ isC(═O)NR^(a)R^(b), wherein R^(a) is hydrogen or optionally substitutedalkyl, and R^(b) is independently optionally substituted alkyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group, orR^(a) and R^(b) are taken together with the nitrogen to form anoptionally substituted heterocyclyl ring.

In certain embodiments, R¹ is —NR^(a)R^(b), wherein R^(a) and R^(b) areas defined herein. In certain embodiments, R¹ is —NR^(a)R^(b), whereineach of R^(a) and R^(b) is independently hydrogen, optionallysubstituted alkyl, optionally substituted carbocyclyl, or a nitrogenprotecting group. In certain embodiments, R¹ is —NR^(a)R^(b), whereinR^(a) is hydrogen, optionally substituted alkyl, or optionallysubstituted carbocyclyl; and R^(b) is independently hydrogen, optionallysubstituted alkyl, or a nitrogen protecting group.

In certain embodiments of Formulae (I)-(III), R¹ is of Formula (n-1):

wherein:

each instance of R^(1a) is independently hydrogen, halogen, optionallysubstituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1);

each instance of R^(N1) is independently hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group;

R^(O1) is independently hydrogen, optionally substituted C₁-C₆ alkyl, oran oxygen protecting group; and

a1 is 0 or an integer between 1 and 6, inclusive.

In certain embodiments, a1 is 1. In certain embodiments, a1 is 2. Incertain embodiments, a1 is 3.

In certain embodiments, R^(1a) is optionally substituted C₁-C₆ alkyl. Incertain embodiments, R^(1a) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1a) is methyl or ethyl. In certain embodiments, R^(1a)is substituted C₁-C₆ alkyl. In certain embodiments, R^(1a) is hydroxyC₁-C₆ alkyl. In certain embodiments, R^(1a) is —CH₂OH. In certainembodiments, R^(1a) is —CH₂CH₂OH. In certain embodiments, R^(1a) is—N(R^(N1))₂, wherein R^(N1) is as defined herein. In certainembodiments, R^(1a) is —NHR^(N1), wherein R^(N1) is as defined herein.In certain embodiments, R^(1a) is —NHR^(N1), wherein R^(N1) is hydrogenor optionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1a) is—NH₂. In certain embodiments, R^(1a) is —NHR^(N1), wherein R^(N1) isoptionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1a) is—NHR^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1a) is —NHR^(N1), wherein R^(N1) is methyl or ethyl. Incertain embodiments, R^(1a) is —NHCH₃. In certain embodiments, R^(1a) is—NHR^(N1), wherein R^(N1) is a nitrogen protecting group. In certainembodiments, R^(1a) is —N(CH₃)R^(N1), wherein R^(N1) is optionallysubstituted C₁-C₆ alkyl. In certain embodiments, R^(1a) is—N(CH₃)R^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1a) is —N(CH₃)R^(N1), wherein R^(N1) is methyl or ethyl.In certain embodiments, R^(1a) is —N(CH₃)₂. In certain embodiments,R^(1a) is —N(CH₃)R^(N1), wherein R^(N1) is a nitrogen protecting group.

In certain embodiments of Formulae (I)-(III), R¹ is —NR^(a)R^(b),wherein R^(a) and R^(b) are joined to form an optionally substitutedheterocyclic or optionally substituted heteroaryl ring. In certainembodiments, R¹ is of one of the following formulae:

wherein:

each instance of R^(NX) is independently hydrogen, optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted aryl, optionally substituted heterocyclyl, optionallysubstituted heteroaryl, or a nitrogen protecting group;

each instance of R^(1b) is independently hydrogen, halogen, optionallysubstituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1);

each instance of R^(N1) is independently hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group;

R^(O1) is independently hydrogen, optionally substituted C₁-C₆ alkyl, oran oxygen protecting group; and

b1 is 0 or an integer between 1 and 6, inclusive, as valency permits.

In certain embodiments, R¹ is of Formula (n-2):

wherein:

each instance of R^(1b) is independently hydrogen, halogen, optionallysubstituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1);

each instance of R^(N1) is independently hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group;

R^(O1) is independently hydrogen, optionally substituted C₁-C₆ alkyl, oran oxygen protecting group; and

b1 is 0 or an integer between 1 and 6, inclusive.

In certain embodiments, b1 is 1. In certain embodiments, b1 is 2. Incertain embodiments, b1 is 3.

In certain embodiments, R^(1b) is optionally substituted C₁-C₆ alkyl. Incertain embodiments, R^(1b) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1b) is methyl or ethyl. In certain embodiments, R^(1b)is substituted C₁-C₆ alkyl. In certain embodiments, R^(1b) is hydroxyC₁-C₆ alkyl. In certain embodiments, R^(1b) is —CH₂OH. In certainembodiments, R^(1b) is —CH₂CH₂OH. In certain embodiments, R^(1b) is—N(R^(N1))₂, wherein R^(N1) is as defined herein. In certainembodiments, R^(1b) is —NHR^(N1), wherein R^(N1) is as defined herein.In certain embodiments, R^(1b) is —NHR^(N1), wherein R^(N1) is hydrogenor optionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1b) is—NH₂. In certain embodiments, R^(1b) is —NHR^(N1), wherein R^(N1) isoptionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1b) is—NHR^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1b) is —NHR^(N1), wherein R^(N1) is methyl or ethyl. Incertain embodiments, R^(1b) is —NHCH₃. In certain embodiments, R^(1b) is—NHR^(N1), wherein R^(N1) is a nitrogen protecting group. In certainembodiments, R^(1b) is —N(CH₃)R^(N1), wherein R^(N1) is optionallysubstituted C₁-C₆ alkyl. In certain embodiments, R^(1b) is—N(CH₃)R^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1b) is —N(CH₃)R^(N1), wherein R^(N1) is methyl or ethyl.In certain embodiments, R^(1b) is —N(CH₃)₂. In certain embodiments,R^(1b) is —N(CH₃)R^(N1), wherein R^(N1) is a nitrogen protecting group.

In certain embodiments, R^(NX) is hydrogen. In certain embodiments,R^(NX) is optionally substituted alkyl. In certain embodiments, R^(NX)is unsubstituted C₁-C₆ alkyl (e.g. methyl or ethyl). In certainembodiments, R^(NX) is substituted C₁-C₆ alkyl. In certain embodiments,R^(NX) is a nitrogen protecting group.

In certain embodiments of Formulae (I)-(III), R¹ is optionallysubstituted carbocyclyl. In certain embodiments, R¹ is optionallysubstituted monocyclic carbocyclyl. In certain embodiments, R¹ isoptionally substituted cyclopentyl. In certain embodiments, R¹ isoptionally substituted cyclohexyl of Formula (n-3)

wherein:

each instance of R^(1c) is independently hydrogen, halogen, optionallysubstituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1);

each instance of R^(N1) is independently hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group;

R^(O1) is independently hydrogen, optionally substituted C₁-C₆ alkyl, oran oxygen protecting group; and

c1 is 0 or an integer between 1 and 6, inclusive.

In certain embodiments, c1 is 1. In certain embodiments, c1 is 2. Incertain embodiments, c1 is 3.

In certain embodiments, R^(1c) is optionally substituted C₁-C₆ alkyl. Incertain embodiments, R^(1c) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1c) is methyl or ethyl. In certain embodiments, R^(1c)is substituted C₁-C₆ alkyl. In certain embodiments, R^(1c) is hydroxyC₁-C₆ alkyl. In certain embodiments, R^(1c) is —CH₂OH. In certainembodiments, R^(1c) is —CH₂CH₂OH. In certain embodiments, R^(1c) is—N(R^(N1))₂, wherein R^(N1) is as defined herein. In certainembodiments, R^(1c) is —NHR^(N1), wherein R^(N1) is as defined herein.In certain embodiments, R^(1c) is —NHR^(N1), wherein R^(N1) is hydrogenor optionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1c) is—NH₂. In certain embodiments, R^(1c) is —NHR^(N1), wherein R^(N1) isoptionally substituted C₁-C₆ alkyl. In certain embodiments, R^(1c) is—NHR^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1c) is —NHR^(N1), wherein R^(N1) is methyl or ethyl. Incertain embodiments, R^(1c) is —NHCH₃. In certain embodiments, R^(1c) is—NHR^(N1), wherein R^(N1) is a nitrogen protecting group. In certainembodiments, R^(1c) is —N(CH₃)R^(N1), wherein R^(N1) is optionallysubstituted C₁-C₆ alkyl. In certain embodiments, R^(1c) is—N(CH₃)R^(N1), wherein R^(N1) is unsubstituted C₁-C₆ alkyl. In certainembodiments, R^(1c) is —N(CH₃)R^(N1), wherein R^(N1) is methyl or ethyl.In certain embodiments, R^(1c) is —N(CH₃)₂. In certain embodiments,R^(1c) is —N(CH₃)R^(N1), wherein R^(N1) is a nitrogen protecting group.

In certain embodiments of Formulae (I)-(III), R¹ is optionallysubstituted aryl. In certain embodiments, R¹ is optionally substitutedmonocyclic aryl. In certain embodiments, R¹ is optionally substitutedphenyl of Formula (n-4)

wherein:

each instance of R^(1d) is independently hydrogen, halogen, —CN, —NO₂,—N₃, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted aryl, optionally substituted heterocyclyl,optionally substituted heteroaryl, —OR^(A), —N(R^(B))₂, —SR^(A),—C(═O)R^(c), —C(═O)OR^(A), —OC(═O)_(R) ^(c), —C(═O)N(R^(B))₂,—NR^(B)C(═O)R^(c), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)OR^(A),—NR^(B)C(═O)N(R^(B))₂, S(═O)R^(c), —SO₂R^(C), —NR^(B)SO₂R^(C), or—SO₂N(R^(B))₂;

each instance of R^(A) is hydrogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, anoxygen protecting group when attached to oxygen, or a sulfur protectinggroup when attached to sulfur;

each instance of R^(B) is independently hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl,optionally substituted acyl, or a nitrogen protecting group, or twoR^(B) groups are taken together with their intervening atoms to form anoptionally substituted heterocyclic ring; and

d1 is 0 or an integer between 1 and 5, inclusive.

In certain embodiments, d1 is 0. In certain embodiments, d1 is 1. Incertain embodiments, d1 is 2. In certain embodiments, d1 is 3.

In certain embodiments, R^(1d) is hydrogen. In certain embodiments,R^(1d) is halogen (e.g. F, Cl, Br, or I). In certain embodiments, R^(1d)is optionally substituted alkyl. In certain embodiments, R^(1d) isunsubstituted alkyl. In certain embodiments, R^(1d) is methyl or ethyl.

As generally defined herein in Formulae (I)-(III), R³ is hydrogen,halogen, or optionally substituted C₁-C₆ alkyl. In certain embodiments,R³ is hydrogen. In certain embodiments, R³ is halogen (e.g. F, Cl, Br,or I). In certain embodiments, R³ is optionally substituted C₁-C₆ alkyl.In certain embodiments, R³ is unsubstituted C₁-C₆ alkyl. In certainembodiments, R³ is methyl, ethyl, n-propyl, or isopropyl. In certainembodiments, R³ is substituted C₁-C₆ alkyl.

As generally defined herein in Formulae (II)-(III), R⁴ is hydrogen,halogen, or optionally substituted C₁-C₆ alkyl. In certain embodiments,R⁴ is hydrogen. In certain embodiments, R⁴ is halogen (e.g. F, Cl, Br,or I). In certain embodiments, R⁴ is optionally substituted C₁-C₆ alkyl.In certain embodiments, R⁴ is unsubstituted C₁-C₆ alkyl. In certainembodiments, R⁴ is methyl, ethyl, n-propyl, or isopropyl. In certainembodiments, R⁴ is substituted C₁-C₆ alkyl.

As generally defined herein in Formula (I), R⁵ is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group. In certainembodiments, R⁵ is hydrogen. In certain embodiments, R⁵ is optionallysubstituted C₁-C₆ alkyl. In certain embodiments, R⁵ is unsubstitutedC₁-C₆ alkyl. In certain embodiments, R⁵ is methyl, ethyl, n-propyl, orisopropyl. In certain embodiments, R⁵ is substituted C₁-C₆ alkyl. Incertain embodiments, R⁵ is nitrogen protecting group. In certainembodiments, R⁵ is nitrogen protecting group.

As generally defined herein in Formulae (I)-(III), L¹ is a bond,—NR^(L1)—(CH₂)_(t)—, —O—, or —S—, wherein R^(L1) is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group, wherein t is 0or an integer between 1 and 5, inclusive. In certain embodiments, L¹ isa bond. In certain embodiments, L¹ is —O—. In certain embodiments, L¹ is—S—. In certain embodiments, L¹ is —NR^(L1)—(CH₂)_(t)—, wherein R^(L1)is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group. In certain embodiments, t is 0. In certainembodiments, t is 1. In certain embodiments, t is 2. In certainembodiments, t is 3. In certain embodiments, t is 4. In certainembodiments, t is 5. In certain embodiments, L¹ is —NR^(L1)—, whereinR^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group. In certain embodiments, L¹ is —NH—. In certainembodiments, L¹ is —NH—. In certain embodiments, L¹ is —NR^(L1)—,wherein R^(L1) is optionally substituted C₁-C₆ alkyl. In certainembodiments, L¹ is —NR^(L1)—, wherein R^(L1) is unsubstituted C₁-C₆alkyl. In certain embodiments, L¹ is —NR^(L1)—, wherein R^(L1) is methylor ethyl. In certain embodiments, L¹ is —NR^(L1)—, wherein R^(L1) issubstituted C₁-C₆ alkyl. In certain embodiments, L¹ is —NR^(L1)—,wherein R^(L1) is a nitrogen protecting group (e.g. Boc). In certainembodiments, L¹ is —NR^(L1)—CH₂—, wherein R^(L1) is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group. In certainembodiments, L¹ is —NHCH₂—. In certain embodiments, L¹ is —NR^(L1)—CH₂—,wherein R^(L1) is optionally substituted C₁-C₆ alkyl. In certainembodiments, L¹ is —NR^(L1)—CH₂—, wherein R^(L1) is unsubstituted C₁-C₆alkyl. In certain embodiments, L¹ is —NR^(L1)—CH₂—, wherein R^(L1) ismethyl or ethyl. In certain embodiments, L¹ is —NR^(L1)—CH₂—, whereinR^(L1) is substituted C₁-C₆ alkyl. In certain embodiments, L¹ is—NR^(L1)—CH₂—, wherein R^(L1) is a nitrogen protecting group (e.g. Boc).

As generally defined herein in Formulae (I)-(III), L² is a bond,optionally substituted C₁₋₄ alkylene, —C(═O)—, —NR^(L2)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group. Incertain embodiments, L² is a bond. In certain embodiments, L² is —O—. Incertain embodiments, L² is —S—. In certain embodiments, L² is optionallysubstituted C₁₋₄ alkylene. In certain embodiments, L² is unsubstitutedC₁₋₄ alkylene. In certain embodiments, L² is —CH₂—. In certainembodiments, L² is —(CH₂)₂—. In certain embodiments, L² is —(CH₂)₃—. Incertain embodiments, L² is —(CH₂)₄—. In certain embodiments, L² is—C(═O)—. In certain embodiments, L² is —NR^(L2)—, wherein R^(L2) ishydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogen protectinggroup. In certain embodiments, L² is —NH—. In certain embodiments, L² is—NH—. In certain embodiments, L² is —NR^(L2)—, wherein R^(L2) isoptionally substituted C₁-C₆ alkyl. In certain embodiments, L² is—NR^(L2)—, wherein R^(L2) is unsubstituted C₁-C₆ alkyl. In certainembodiments, L² is —NR^(L2)—, wherein R^(L2) is methyl or ethyl. Incertain embodiments, L² is —NR^(L2)—, wherein R^(L2) is substitutedC₁-C₆ alkyl. In certain embodiments, L² is —NR^(L2)—, wherein R^(L2) isa nitrogen protecting group (e.g. Boc). In certain embodiments, L² is—C(═O)NR^(L2)—, wherein R^(L2) is hydrogen, optionally substituted C₁-C₆alkyl, or a nitrogen protecting group. In certain embodiments, L² is—C(═O)NH—. In certain embodiments, L² is —C(═O)NR^(L2)—, wherein R^(L2)is optionally substituted C₁-C₆ alkyl. In certain embodiments, L² is—C(═O)NR^(L2)—, wherein R^(L2) is unsubstituted C₁-C₆ alkyl. In certainembodiments, L² is —C(═O)NR^(L2)—, wherein R^(L2) is methyl or ethyl. Incertain embodiments, L² is —C(═O)NR^(L2)—, wherein R^(L2) is substitutedC₁-C₆ alkyl. In certain embodiments, L² is —C(═O)NR^(L2)—, whereinR^(L2) is a nitrogen protecting group (e.g. Boc). In certainembodiments, L² is —NR^(L2)C(═O)—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protecting group. Incertain embodiments, L² is —NHC(═O)—. In certain embodiments, L² is—NR²C(═O)—, wherein R^(L2) is optionally substituted C₁-C₆ alkyl. Incertain embodiments, L² is —NR²C(═O)—, wherein R^(L2) is unsubstitutedC₁-C₆ alkyl. In certain embodiments, L² is —NR^(L2)C(═O)—, whereinR^(L2) is methyl or ethyl. In certain embodiments, L² is —NR^(L2)C(═O)—,wherein R^(L2) is substituted C₁-C₆ alkyl. In certain embodiments, L² is—NR^(L2)C(═O)—, wherein R^(L2) is a nitrogen protecting group (e.g.Boc).

In certain embodiments of Formula (I), R³ is hydrogen and R⁵ isoptionally substituted C₁-C₆ alkyl or a nitrogen protecting group. Incertain embodiments of Formula (I), R³ is hydrogen and R⁵ is optionallysubstituted C₁-C₆ alkyl. In certain embodiments of Formula (I), R³ ishydrogen and R⁵ is unsubstituted C₁-C₆ alkyl. In certain embodiments ofFormula (I), R³ is hydrogen and R⁵ is methyl, ethyl, n-propyl, orisopropyl.

In certain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴is optionally substituted C₁-C₆ alkyl or a nitrogen protecting group. Incertain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴ isoptionally substituted C₁-C₆ alkyl. In certain embodiments of Formula(II) or (III), R³ is hydrogen and R⁴ is unsubstituted C₁-C₆ alkyl. Incertain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴ ismethyl, ethyl, n-propyl, or isopropyl.

In certain embodiments of Formula (I), R¹ is optionally substitutedcarbocyclyl; R³ is hydrogen; and R⁵ is optionally substituted C₁-C₆alkyl or a nitrogen protecting group. In certain embodiments of Formula(I), R¹ is optionally substituted cyclohexyl; R³ is hydrogen; and R⁵ isoptionally substituted C₁-C₆ alkyl. In certain embodiments of Formula(I), R¹ is mono-substituted cyclohexyl; R³ is hydrogen; and R⁵ isunsubstituted C₁-C₆ alkyl. In certain embodiments of Formula (I), R¹ isoptionally substituted aryl; R³ is hydrogen; and R⁵ is optionallysubstituted C₁-C₆ alkyl or a nitrogen protecting group. In certainembodiments of Formula (I), R¹ is optionally substituted phenyl; R³ ishydrogen; and R⁵ is optionally substituted C₁-C₆ alkyl. In certainembodiments of Formula (I), R¹ is mono-substituted phenyl; R³ ishydrogen; and R⁵ is unsubstituted C₁-C₆ alkyl. In certain embodiments ofFormula (I), R¹ is —NR^(a)R^(b), wherein R^(a) and R^(b) are as definedherein; R³ is hydrogen; and R⁵ is optionally substituted C₁-C₆ alkyl ora nitrogen protecting group. In certain embodiments of Formula (I), R¹is —NR^(a)R^(b), wherein R^(a) is optionally substituted carbocyclyl andR^(b) is hydrogen or optionally substituted alkyl; R³ is hydrogen; andR⁵ is optionally substituted C₁-C₆ alkyl. In certain embodiments ofFormula (I), R¹ is —NR^(a)R^(b), wherein R^(a) is optionally substitutedcyclohexyl and R^(b) is hydrogen; R³ is hydrogen; and R⁵ isunsubstituted C₁-C₆ alkyl. In certain embodiments of Formula (I), R¹ is—NR^(a)R^(b), wherein R^(a) and R^(b) are joined to form an optionallysubstituted heterocylic ring; R³ is hydrogen; and R⁵ is optionallysubstituted C₁-C₆ alkyl. In certain embodiments of Formula (I), R¹ is—NR^(a)R^(b), wherein R^(a) and R^(b) are joined to form an optionallysubstituted piperidine ring; R³ is hydrogen; and R⁵ is unsubstitutedC₁-C₆ alkyl. In certain embodiments of Formula (I), R¹ is —NR^(a)R^(b),wherein R^(a) and R^(b) are joined to form a mono-substituted piperidinering; R³ is hydrogen; and R⁵ is unsubstituted C₁-C₆ alkyl.

In certain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴is optionally substituted C₁-C₆ alkyl or a nitrogen protecting group. Incertain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴ isoptionally substituted C₁-C₆ alkyl. In certain embodiments of Formula(II) or (III), R³ is hydrogen and R⁴ is unsubstituted C₁-C₆ alkyl. Incertain embodiments of Formula (II) or (III), R³ is hydrogen and R⁴ ismethyl, ethyl, n-propyl, or isopropyl.

In certain embodiments of Formula (II) or (III), R¹ is optionallysubstituted carbocyclyl; R³ is hydrogen; and R⁴ is optionallysubstituted C₁-C₆ alkyl or a nitrogen protecting group. In certainembodiments of Formula (II) or (III), R¹ is optionally substitutedcyclohexyl; R³ is hydrogen; and R⁴ is optionally substituted C₁-C₆alkyl. In certain embodiments of Formula (II) or (III), R¹ ismono-substituted cyclohexyl; R³ is hydrogen and R⁴ is unsubstitutedC₁-C₆ alkyl. In certain embodiments of Formula (II) or (III), R¹ isoptionally substituted aryl; R³ is hydrogen and R⁴ is optionallysubstituted C₁-C₆ alkyl or a nitrogen protecting group. In certainembodiments of Formula (II) or (III), R¹ is optionally substitutedphenyl; R³ is hydrogen; and R⁴ is optionally substituted C₁-C₆ alkyl. Incertain embodiments of Formula (II) or (III), R¹ is mono-substitutedphenyl; R³ is hydrogen; and R⁴ is unsubstituted C₁-C₆ alkyl. In certainembodiments of Formula (II) or (III), R¹ is —NR^(a)R^(b), wherein R^(a)and R^(b) are as defined herein; R³ is hydrogen; and R⁴ is optionallysubstituted C₁-C₆ alkyl or a nitrogen protecting group. In certainembodiments of Formula (II) or (III), R¹ is —NR^(a)R^(b), wherein R^(a)is optionally substituted carbocyclyl and R^(b) is hydrogen oroptionally substituted alkyl; R³ is hydrogen and R⁴ is optionallysubstituted C₁-C₆ alkyl. In certain embodiments of Formula (II) or(III), R¹ is —NR^(a)R^(b), wherein R^(a) is optionally substitutedcyclohexyl and R^(b) is hydrogen; R³ is hydrogen; and R⁴ isunsubstituted C₁-C₆ alkyl. In certain embodiments of Formula (II) or(III), R¹ is —NR^(a)R^(b), wherein R^(a) and R^(b) are joined to form anoptionally substituted heterocylic ring; R³ is hydrogen; and R⁴ isoptionally substituted C₁-C₆ alkyl. In certain embodiments of Formula(II) or (III), R¹ is —NR^(a)R^(b), wherein R^(a) and R^(b) are joined toform an optionally substituted piperidine ring; R³ is hydrogen; and R⁴is unsubstituted C₁-C₆ alkyl. In certain embodiments of Formula (II) or(III), R¹ is —NR^(a)R^(b), wherein R^(a) and R^(b) are joined to form amono-substituted piperidine ring; R³ is hydrogen; and R⁴ is methyl,ethyl, n-propyl, or isopropyl.

Compounds of any one of Formulae (I)-(III) include Ring A between linkerL¹ and linker L². Ring A may be optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl. In certain embodiments, Ring A isoptionally substituted carbocyclyl. In certain embodiments, Ring A isoptionally substituted heterocyclyl. In certain embodiments, Ring A isoptionally substituted aryl. In certain embodiments, Ring A isoptionally substituted heteroaryl. In certain embodiments, Ring A isoptionally substituted phenyl. In certain embodiments, Ring A is phenylsubstituted with only L¹ and L². In certain embodiments, Ring A isoptionally substituted cyclohexyl. In certain embodiments, Ring A isoptionally substituted piperidinyl. In certain embodiments, Ring A isoptionally substituted piperizinyl. In certain embodiments, Ring A isoptionally substituted pyridinyl. In certain embodiments, Ring A isoptionally substituted pyrimidinyl.

In certain embodiments of Formulae (I)-(III), linkers L¹ and L² areattached “ortho” or 1,2 to Ring A. In certain embodiments, linkers L¹and L² are attached “meta” or 1,3 to Ring A. In certain embodiments,linkers L¹ and L² are attached “para” or 1,4 to ring A.

In certain embodiments of Formulae (I)-(III), Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position.

In certain embodiments of Formulae (I)-(III), Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

L¹ and L² may attach to ring A at either indicated position. In certainembodiments, Ring A is

wherein L¹ is attached to position a and L² is attached to position b.In certain embodiments, Ring A is

wherein L² is attached to position a and L¹ is attached to position b.In certain embodiments, Ring A is

wherein L¹ and L² may attach to ring A at either indicated position. Incertain embodiments, Ring A is

wherein L¹ and L² may attach to ring A at either indicated position.

Compounds of Formulae (I)-(III) include Ring B between linker L² andgroup R². In certain embodiments, linker L² is a bond, such that Ring Bis directly attached to Ring A. Ring B may absent, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, or optionally substituted heteroaryl. In certainembodiments, Ring B is absent, such that L² is directly attached to R².In certain embodiments, Ring B is absent and linker L² is a bond, suchthat Ring A is directly attached to R². In certain embodiments, Ring Bis optionally substituted carbocyclyl. In certain embodiments, Ring B isoptionally substituted heterocyclyl. In certain embodiments, Ring B isoptionally substituted aryl. In certain embodiments, Ring B isoptionally substituted heteroaryl. In certain embodiments, Ring B isoptionally substituted phenyl. In certain embodiments, Ring B isoptionally substituted cyclohexyl. In certain embodiments, Ring B isoptionally substituted piperidinyl. In certain embodiments, Ring B isoptionally substituted piperizinyl. In certain embodiments, Ring B isoptionally substituted pyridinyl. In certain embodiments, Ring B isoptionally substituted pyrimidinyl.

In certain embodiments of Formulae (I)-(III), linker L² and group R² areattached “ortho” or 1,2 to each other on Ring B. In certain embodiments,linkers L² and group R² are attached “meta” or 1,2 to each other on RingB. In certain embodiments, linkers L² and R² are attached “para” or 1,4to each other on Ring B.

In certain embodiments of Formulae (I)-(III), Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position.

In certain embodiments of Formulae (I)-(III), Ring B is

In certain embodiments, Ring B is

In certain embodiments, Ring B is

In certain embodiments, Ring B is

L² and R² may attach to Ring B at either indicated position. In certainembodiments, Ring B is

wherein L² and R² may attach to Ring B at either indicated position. Incertain embodiments, Ring B is

wherein L² and R² may attach to Ring B at either indicated position.

Compounds of Formulae (I)-(III) include R² attached to Ring B. Incertain embodiments, Ring B is absent, such that R² is directly attachedto linker L². In certain embodiments, Ring B is absent and L² is a bond,such that R² is directly attached to Ring A. In certain embodiments, R²comprises an electrophilic moiety. In certain embodiments, R² comprisesa Michael acceptor moiety. The electrophilic moiety (e.g., Michaelacceptor moiety) may react with a cysteine residue of a kinase (e.g.,CDK (e.g., CDK7)) to allow for covalent attachment of the compound tothe kinase. In certain embodiments, the electrophilic moiety (e.g.,Michael acceptor moiety) may react with a cysteine residue of a kinase(e.g., CDK (e.g., CDK7)). In certain embodiments, the electrophilicmoiety (e.g., Michael acceptor moiety) may react with the Cys312 residueof CDK7. In certain embodiments, the covalent attachment isirreversible. In certain embodiments, the covalent attachment isreversible.

As generally defined herein in Formulae (I)-(III), R² may be any one ofFormulae (i-1)-(i-41). In certain embodiments, R² is of Formula (i-1):

In certain embodiments, R² is of Formula (i-2):

In certain embodiments, R² is of Formula (i-3):

In certain embodiments, R² is of Formula (i-4):

In certain embodiments, R² is of Formula (i-5):

In certain embodiments, R² is of Formula (i-6):

In certain embodiments, R² is of Formula (i-7):

In certain embodiments, R² is of Formula (i-8):

In certain embodiments, R² is of Formula (i-9):

In certain embodiments, R² is of Formula (i-10):

In certain embodiments, R² is of Formula (i-11):

In certain embodiments, R² is of Formula (i-12):

In certain embodiments, R² is of Formula (i-13):

In certain embodiments, R² is of Formula (i-14):

In certain embodiments, R² is of Formula (i-15):

In certain embodiments, R² is of Formula (i-16):

In certain embodiments, R² is of Formula (i-17):

In certain embodiments, R² is of Formula (i-18):

In certain embodiments, R² is of Formula (i-19):

In certain embodiments, R² is of Formula (i-20):

In certain embodiments, R² is of Formula (i-21):

In certain embodiments, R² is of Formula (i-22):

In certain embodiments, R² is of Formula (i-23):

In certain embodiments, R² is of Formula (i-24):

In certain embodiments, R² is of Formula (i-25):

In certain embodiments, R² is of Formula (i-26):

In certain embodiments, R² is of Formula (i-27):

In certain embodiments, R² is of Formula (i-28):

In certain embodiments, R² is of Formula (i-29):

In certain embodiments, R² is of Formula (i-30):

In certain embodiments, R² is of Formula (i-31):

In certain embodiments, R² is of Formula (i-32):

In certain embodiments, R² is of Formula (i-33):

In certain embodiments, R² is of Formula (i-34):

In certain embodiments, R² is of Formula (i-35):

In certain embodiments, R² is of Formula (i-36):

In certain embodiments, R² is of Formula (i-37):

In certain embodiments, R² is of Formula (i-38):

In certain embodiments, R² is of Formula (i-39):

In certain embodiments, R² is of Formula (i-40):

In certain embodiments, R² is of Formula (i-41):

In certain embodiments, R² is of Formula (i-1a):

In certain embodiments, R² is of Formula (i-1b):

In certain embodiments, R² is of Formula (i-1c):

In certain embodiments, R² is of Formula (i-1d):

In certain embodiments, R² is of Formula (i-1e):

In certain embodiments, R² is of Formula (i-1f):

In certain embodiments, R² is of Formula (i-1g):

In certain embodiments, R² is

In certain embodiments, R² is of Formula (i-1h):

In certain embodiments, R² is

In certain embodiments, R² is of Formula (i-1a):

In certain embodiments, R² is of Formula (i-1b):

In certain embodiments, R² is of Formula (i-1c):

In certain embodiments, R² is of Formula (i-18a):

In certain embodiments, R² is of Formula (i-18b):

In certain embodiments, R² is of Formula (i-18c)

In certain embodiments, R² is of Formula (i-15a):

In certain embodiments, R² is of Formula (i-15b):

In certain embodiments, R² is of Formula (i-15c):

R² may contain linker L³ or L⁴. In certain embodiments, L³ is a bond. L³is an optionally substituted C₁₋₄ hydrocarbon chain. In certainembodiments, L³ is an optionally substituted C₁₋₄ hydrocarbon chain,wherein one or more carbon units of the hydrocarbon chain areindependently replaced with —C(═O)—, —O—, —S—, —NR^(L3a)—,—NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—. In certain embodiments, L³ is anoptionally substituted C₁₋₄ hydrocarbon chain, wherein one carbon unitof the hydrocarbon chain is replaced with —NR^(L3a)— (e.g., —NH—). Incertain embodiments, L³ is of the formula: —(CH₂)₁₋₄—NR^(L3a)— (e.g.,—(CH₂)₁₋₄—NH—) or —NR^(L3a)—CH₂)₁₋₄— (e.g., —NH—CH₂)₁₋₄—). In certainembodiments, L³ is —NR^(L3a)—. In certain embodiments, L³ is—NR^(L3a)(C═O)—. In certain embodiments, L³ is —(C═O)NR^(L3a)—. Incertain embodiments, L³ is —NH—. In certain embodiments, L³ is —(C═O)—.In certain embodiments, L³ is —NH(C═O)—. In certain embodiments, L³ is—(C═O)NH—. In certain embodiments, L³ is —O—. In certain embodiments, L³is —S—. In certain embodiments, L⁴ is a bond. In certain embodiments, L⁴is an optionally substituted C₁₋₄ hydrocarbon chain.

Linker L³ may contain groups R^(L3a) or R^(L3b). In certain embodiments,R^(L3a) is hydrogen. In certain embodiments, at least one instance ofR^(L3b) is hydrogen. In certain embodiments, each instance of R^(L3b) ishydrogen. In certain embodiments, at least one instance of R^(L3b) is—Cl, —Br, or —I. In certain embodiments, each instance of R^(L3b) is—Cl, —Br, or —I. In certain embodiments, at least one instance ofR^(L3b) is —F. In certain embodiments, each instance of R^(L3b) is —F.In certain embodiments, at least one instance of R^(L3b) is optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl. In certain embodiments, two R^(L3b) groups arejoined to form an optionally substituted carbocyclic or optionallysubstituted heterocyclic ring.

R² may contain groups R^(E1), R^(E2), and/or R^(E3). In certainembodiments, R^(E1) is hydrogen. In certain embodiments, R^(E2) ishydrogen. In certain embodiments, R^(E3) is hydrogen. In certainembodiments, R^(E1) is —Cl, —Br, or —I. In certain embodiments, R^(E2)is —Cl, —Br, or —I. In certain embodiments, R^(E3) is —Cl, —Br, or —I.In certain embodiments, R^(E1) is —F. In certain embodiments, R^(E2) is—F. In certain embodiments, R^(E3) is —F. In certain embodiments, R^(E1)is optionally substituted alkyl (e.g., substituted or unsubstituted C₁₋₆alkyl). In certain embodiments, R^(E2) is optionally substituted alkyl(e.g., substituted or unsubstituted C₁₋₆ alkyl). In certain embodiments,R^(E3) is optionally substituted alkyl (e.g., substituted orunsubstituted C₁₋₆ alkyl). In certain embodiments, R^(E1) is optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, or—SR^(EE). In certain embodiments, R^(E2) is optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₃, —Si(R^(EE))₃, or—SR^(EE). In certain embodiments, R^(E3) is optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, orSR^(EE). In certain embodiments, R^(E1) is —N(R^(EE))₂. In certainembodiments, R^(E2) is —N(R^(EE))₂. In certain embodiments, R^(E3) is—N(R^(EE))₂. In certain embodiments, R^(E1) is —N(CH₃)₂. In certainembodiments, R^(E2) is —N(CH₃)₂. In certain embodiments, R^(E3) is—N(CH₃)₂. In certain embodiments, R^(E1) is —CH₂N(R^(EE))₂. In certainembodiments, R^(E2) is —CH₂N(R^(EE))₂. In certain embodiments, R^(E3) is—CH₂N(R^(EE))₂. In certain embodiments, R^(E1) is —CH₂N(CH₃)₂. Incertain embodiments, R^(E2) is —CH₂N(CH₃)₂. In certain embodiments,R^(E3) is —CH₂N(CH₃)₂. In certain embodiments, R^(E1) is —CN. In certainembodiments, R^(E2) is —CN. In certain embodiments, R^(E3) is —CN.

In certain embodiments, R^(E1) and R^(E3) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E1)and R^(E3) are joined to form an optionally substituted heterocyclicring. In certain embodiments, R^(E2) and R^(E3) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E2)and R^(E3) are joined to form an optionally substituted heterocyclicring. In certain embodiments, R^(E1) and R^(E2) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E1)and R^(E2) are joined to form an optionally substituted heterocyclicring.

R² may contain group R^(E4), where R^(E4) is a leaving group. In certainembodiments, R^(E4) is —Cl, —Br, or —I. In certain embodiments, R^(E4)is —F. In certain embodiments, R^(E4) is —OS(═O)R^(E4a) or—OS(═O)₂R^(E4a), wherein R^(E4a) is substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted carbocyclyl, substituted orunsubstituted heterocyclyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. In certain embodiments, R^(E4)is —OR^(E4a). In certain embodiments, R^(E4) is —OMs, —OTf, —OTs, —OBs,or 2-nitrobenzenesulfonyloxy. In certain embodiments, R^(E4) is—OR^(E4a). In certain embodiments, R^(E4) is —OMe, —OCF₃, or —OPh. Incertain embodiments, R^(E4) is —OC(═O)R^(E4a). In certain embodiments,R^(E4) is —OC(═O)Me, —OC(═O)CF₃, —OC(═O)Ph, or —OC(═O)Cl. In certainembodiments, R^(E4) is —OC(═O)OR^(E4a). In certain embodiments, R^(E4)is —OC(═O)OMe or —OC(═O)O(t-Bu).

R² may contain group R^(E5), where R^(EE) is a halogen. In certainembodiments, R^(EE) is —Cl, —Br, or —I. In certain embodiments, R^(EE)is —F.

R² may contain group R^(E6). In certain embodiments, R^(E6) is hydrogen.In certain embodiments, R^(E6) is substituted or unsubstituted C₁-C₆alkyl. In certain embodiments, R^(E6) is a nitrogen protecting group.

In certain embodiments, a is 1. In certain embodiments, a is 2.

In certain embodiments, z is 0. In certain embodiments, z is 1. Incertain embodiments, z is 2. In certain embodiments, z is 3, 4, 5, or 6.

R² may contain group Y. In certain embodiments, Y is 0. In certainembodiments, Y is S. In certain embodiments, Y is NR^(E7). In certainembodiments, Y is NH.

Compounds of Formula (I) may exist as tautomers or mixtures thereof ofFormulae (I-a) and (I-b):

In each tautomer, R⁵ is attached to different imidazole nitrogens incompounds of each formula. In certain embodiments, R⁵ is attached to thenitrogen at the position labeled 9, as in Formula (I-a). In certainembodiments, R⁵ is attached to the nitrogen at the position labeled 7,as in Formula (I-b). In certain embodiments, compounds of Formula (I)may exist as a mixture of compounds of Formulae (I-a) and (I-b), inwhich case R⁵ is attached to the nitrogen at the position labeled 9 forcomponents of the mixture corresponding to Formula (I-a), and R⁵ isattached to the nitrogen at the position labeled 7 for components of themixture corresponding to Formula (I-b).

In certain embodiments, a compound of Formula (I) is of Formula (I-1):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein L¹, L², Ring A, Ring B, R², R⁵, R^(b), R^(1a),and a1 are as defined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-1-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R2, R5, R^(L1), R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-1-a-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R⁵, R^(L1), R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-1-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R⁵, R^(L1), R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-1-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R⁵, R^(L1), R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-1-b-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R⁵, R^(L1), R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-1-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R⁵, R^(L1), R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-1-c-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R⁵, R^(L1), R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-2):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², L¹, Ring A, Ring B, R⁵, R^(1b), and b1are as defined herein

In certain embodiments, a compound of Formula (I) is of Formula (I-2-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁵, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (I) is of Formula(I-2-a-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁵, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (I) is of Formula (I-2-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁵, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-2-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁵, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula(I-2-b-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁵, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-3):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², L¹, Ring A, Ring B, R⁵, R^(1c), and c1are as defined herein.

In certain embodiments, a compound of Formula (I) is of Formula (I-3-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, R⁵, R^(1c), and c1 are as definedherein.

In certain embodiments, a compound of Formula (I) is of Formula(I-3-a-1):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, R⁵, R^(1c), and c1 are as definedherein.

In certain embodiments, a compound of Formula (I) is of Formula (I-3-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, R⁵, R^(1c), and c1 are as definedherein.

In certain embodiments, a compound of Formula (II) is of Formula(I-3-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, R⁵, R^(1c), and c1 are as definedherein.

In certain embodiments, a compound of Formula (I) is one of thefollowing formulae:

In certain embodiments, a compound of Formula (II) is of Formula (II-1):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, L², Ring A, Ring B, R⁴, R^(b), R^(1a),and a1 are as defined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-1-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-1-a-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-1-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-1-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-1-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (II) is of Formula (II-2):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, L², Ring A, Ring B, R⁴, R^(1b), and b1are as defined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-d-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of Formula(II-2-d-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (II) is of one of thefollowing formulae:

In certain embodiments, a compound of Formula (II) is of one of thefollowing formulae:

In certain embodiments, a compound of Formula (II) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound of Formula (II) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound of Formula (III) is of Formula(III-1):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², L¹, Ring A, Ring B, R⁴, R^(b), R^(1a),and a1 are as defined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-a-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(b), R^(1a), and a1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-c-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-1-c-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(b), R^(1a), and a1 areas defined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L¹, L², Ring A, Ring B, R⁴, R^(1b), and b1are as defined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-a-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-a-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-b-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(L1), R⁴, R^(1b), and b1 are as definedherein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-d-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of Formula(III-2-d-ii):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², L², R^(L1), R⁴, R^(1b), and b1 are asdefined herein.

In certain embodiments, a compound of Formula (III) is of one of thefollowing formulae:

In certain embodiments, a compound of Formula (III) is of one of thefollowing formulae:

In certain embodiments, a compound of Formula (III) is of the formula:

In certain embodiments, a compound of Formula (III) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (II) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (II) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (III) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In some embodiments, a compound of Formula (III) is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.Pharmaceutical Compositions, Kits, and Administration

The pharmaceutical compositions described herein are useful in treatingand/or preventing proliferative diseases (e.g., cancers (e.g., leukemia,acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma,multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, braincancer, neuroblastoma, lung cancer, colorectal cancer), benignneoplasms, diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases) in a subject. Thecompositions described herein are also useful for inhibiting theactivity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/orCDK13)) in a subject, biological sample, tissue, or cell. Thecompositions described herein are also useful for inducing apoptosis ina cell.

The present disclosure provides pharmaceutical compositions comprising acompound described herein (e.g., a compound of any one of Formulae(I)-(III)), or a pharmaceutically acceptable salt, solvate, hydrate,polymorph, co-crystal, tautomer, stereoisomer, isotopically labeledderivative, or prodrug thereof, and optionally a pharmaceuticallyacceptable excipient. In certain embodiments, the pharmaceuticalcomposition of the invention comprises a compound described herein, or apharmaceutically acceptable salt thereof, and optionally apharmaceutically acceptable excipient. In certain embodiments, apharmaceutical composition described herein comprises a compounddescribed herein, or a pharmaceutically acceptable salt thereof, and apharmaceutically acceptable excipient. In certain embodiments, thecompound described herein, or a pharmaceutically acceptable salt,solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer,isotopically labeled derivative, or prodrug thereof, is provided in aneffective amount in the pharmaceutical composition.

In certain embodiments, the effective amount is a therapeuticallyeffective amount (e.g., amount effective for treating a proliferativedisease in a subject in need thereof). In certain embodiments, theeffective amount is an amount effective for inhibiting the activity of aprotein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in asubject in need thereof. In certain embodiments, the effective amount isan amount effective for inhibiting the activity of a protein kinase(e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a cell. In certainembodiments, the effective amount is an amount effective for inducingapoptosis in a cell. In certain embodiments, the effective amount is aprophylactically effective amount (e.g., amount effective for preventinga proliferative disease in a subject in need thereof and/or for keepinga subject in need thereof in remission of a proliferative disease).

In certain embodiments, a protein kinase described herein is a CDK. Incertain embodiments, a protein kinase described herein is CDK1, CDK2,CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13,CDK14, CDK15, CDK16, CDK17, CDK18, CDK19, or CDK20. In certainembodiments, a protein kinase described herein is CDK7. In certainembodiments, a protein kinase described herein is CDK12. In certainembodiments, a protein kinase described herein is CDK13. In certainembodiments, a protein kinase described herein is a Src family kinase.In certain embodiments, a protein kinase described herein is SRC. Incertain embodiments, a protein kinase described herein is FGR. Incertain embodiments, a protein kinase described herein is BUB1B. Incertain embodiments, a protein kinase described herein is CHEK2. Incertain embodiments, a protein kinase described herein is HIPK4. Incertain embodiments, a protein kinase described herein is PRKCQ. Incertain embodiments, a protein kinase described herein is RET. Incertain embodiments, a protein kinase described herein is MELK. Incertain embodiments, a protein kinase described herein is IRAK1, IRAK4,BMX, or PI3K. In certain embodiments, a protein kinase described hereinis ABL, ARG, BLK, CSK, EphB1, EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN,MAP2K5, NLK, p38a, SNRK, or TEC. In certain embodiments, a proteinkinase described herein is ABL1(H396P)-phosphorylated,ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FGR,JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC,YES, ABL1(H396P)-nonphosphorylated, ABL1(Y253F)-phosphorylated,ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR¹,EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8,MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN,LCK, EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q),ERBB2, ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del,A750P), CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR,KIT-autoinhibited, or EGFR(E746-A750del). In certain embodiments, aprotein kinase described herein is ABL1(F317L)-nonphosphorylated,ABL1(H396P)-nonphosphorylated, ABL1(H396P)-phosphorylated,ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4,JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB,SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3,FGR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR¹, EPHA2,ABL1(Q252H)-phosphorylated, MEK5, ABL1(Q252H)-nonphosphorylated, ABL2,FYN, EPHB1, ABL1(E255K)-phosphorylated, ABL1(F317L)-phosphorylated,EPHA1, ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5,EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V),KIT-autoinhibited, EGFR(L747-T751del,Sins), EGFR(L858R),EGFR(L747-E749del, A750P), or CSF1R.

In certain embodiments, the effective amount is an amount effective forinhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7,CDK12, and/or CDK13)) by at least about 10%, at least about 20%, atleast about 30%, at least about 40%, at least about 50%, at least about60%, at least about 70%, at least about 80%, at least about 90%, atleast about 95%, or at least about 98%. In certain embodiments, theeffective amount is an amount effective for inhibiting the activity of aprotein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by not morethan 10%, not more than 20%, not more than 30%, not more than 40%, notmore than 50%, not more than 60%, not more than 70%, not more than 80%,not more than 90%, not more than 95%, or not more than 98%. In certainembodiments, the effective amount is an amount effective for inhibitingthe activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/orCDK13)) by a range between a percentage described in this paragraph andanother percentage described in this paragraph, inclusive.

Pharmaceutical compositions described herein can be prepared by anymethod known in the art of pharmacology. In general, such preparatorymethods include bringing the compound described herein (i.e., the“active ingredient”) into association with a carrier or excipient,and/or one or more other accessory ingredients, and then, if necessaryand/or desirable, shaping, and/or packaging the product into a desiredsingle- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold inbulk, as a single unit dose, and/or as a plurality of single unit doses.A “unit dose” is a discrete amount of the pharmaceutical compositioncomprising a predetermined amount of the active ingredient. The amountof the active ingredient is generally equal to the dosage of the activeingredient which would be administered to a subject and/or a convenientfraction of such a dosage, such as one-half or one-third of such adosage.

Relative amounts of the active ingredient, the pharmaceuticallyacceptable excipient, and/or any additional ingredients in apharmaceutical composition described herein will vary, depending uponthe identity, size, and/or condition of the subject treated and furtherdepending upon the route by which the composition is to be administered.The composition may comprise between 0.1% and 100% (w/w) activeingredient.

Pharmaceutically acceptable excipients used in the manufacture ofprovided pharmaceutical compositions include inert diluents, dispersingand/or granulating agents, surface active agents and/or emulsifiers,disintegrating agents, binding agents, preservatives, buffering agents,lubricating agents, and/or oils. Excipients such as cocoa butter andsuppository waxes, coloring agents, coating agents, sweetening,flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calciumphosphate, dicalcium phosphate, calcium sulfate, calcium hydrogenphosphate, sodium phosphate lactose, sucrose, cellulose,microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodiumchloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

Exemplary granulating and/or dispersing agents include potato starch,corn starch, tapioca starch, sodium starch glycolate, clays, alginicacid, guar gum, citrus pulp, agar, bentonite, cellulose, and woodproducts, natural sponge, cation-exchange resins, calcium carbonate,silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone)(crospovidone), sodium carboxymethyl starch (sodium starch glycolate),carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose(croscarmellose), methylcellulose, pregelatinized starch (starch 1500),microcrystalline starch, water insoluble starch, calcium carboxymethylcellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate,quaternary ammonium compounds, and mixtures thereof.

Exemplary surface active agents and/or emulsifiers include naturalemulsifiers (e.g., acacia, agar, alginic acid, sodium alginate,tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk,casein, wool fat, cholesterol, wax, and lecithin), colloidal clays(e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminumsilicate)), long chain amino acid derivatives, high molecular weightalcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetinmonostearate, ethylene glycol distearate, glyceryl monostearate, andpropylene glycol monostearate, polyvinyl alcohol), carbomers (e.g.,carboxy polymethylene, polyacrylic acid, acrylic acid polymer, andcarboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g.,carboxymethylcellulose sodium, powdered cellulose, hydroxymethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose,methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylenesorbitan monolaurate (Tween® 20), polyoxyethylene sorbitan (Tween® 60),polyoxyethylene sorbitan monooleate (Tween® 80), sorbitan monopalmitate(Span® 40), sorbitan monostearate (Span® 60), sorbitan tristearate(Span® 65), glyceryl monooleate, sorbitan monooleate (Span® 80),polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj® 45),polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil,polyoxymethylene stearate, and Solutol®), sucrose fatty acid esters,polyethylene glycol fatty acid esters (e.g., Cremophor®),polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij® 30)),poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamineoleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyllaurate, sodium lauryl sulfate, Pluronic® F-68, poloxamer P-188,cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride,docusate sodium, and/or mixtures thereof.

Exemplary binding agents include starch (e.g., cornstarch and starchpaste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin,molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums(e.g., acacia, sodium alginate, extract of Irish moss, panwar gum,ghatti gum, mucilage of isapol husks, carboxymethylcellulose,methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl methylcellulose, microcrystalline cellulose,cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate(Veegum®), and larch arabogalactan), alginates, polyethylene oxide,polyethylene glycol, inorganic calcium salts, silicic acid,polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.

Exemplary preservatives include antioxidants, chelating agents,antimicrobial preservatives, antifungal preservatives, antiprotozoanpreservatives, alcohol preservatives, acidic preservatives, and otherpreservatives. In certain embodiments, the preservative is anantioxidant. In other embodiments, the preservative is a chelatingagent.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, ascorbylpalmitate, butylated hydroxyanisole, butylated hydroxytoluene,monothioglycerol, potassium metabisulfite, propionic acid, propylgallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, andsodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid(EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodiumedetate, trisodium edetate, calcium disodium edetate, dipotassiumedetate, and the like), citric acid and salts and hydrates thereof(e.g., citric acid monohydrate), fumaric acid and salts and hydratesthereof, malic acid and salts and hydrates thereof, phosphoric acid andsalts and hydrates thereof, and tartaric acid and salts and hydratesthereof. Exemplary antimicrobial preservatives include benzalkoniumchloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide,cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol,chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea,phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate,propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methylparaben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoicacid, potassium benzoate, potassium sorbate, sodium benzoate, sodiumpropionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol,phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate,and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E,beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbicacid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroximemesylate, cetrimide, butylated hydroxyanisol (BHA), butylatedhydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS),sodium lauryl ether sulfate (SLES), sodium bisulfite, sodiummetabisulfite, potassium sulfite, potassium metabisulfite, Glydant®Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, Neolone®,Kathon®, and Euxyl®.

Exemplary buffering agents include citrate buffer solutions, acetatebuffer solutions, phosphate buffer solutions, ammonium chloride, calciumcarbonate, calcium chloride, calcium citrate, calcium glubionate,calcium gluceptate, calcium gluconate, D-gluconic acid, calciumglycerophosphate, calcium lactate, propanoic acid, calcium levulinate,pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasiccalcium phosphate, calcium hydroxide phosphate, potassium acetate,potassium chloride, potassium gluconate, potassium mixtures, dibasicpotassium phosphate, monobasic potassium phosphate, potassium phosphatemixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodiumcitrate, sodium lactate, dibasic sodium phosphate, monobasic sodiumphosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide,aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline,Ringer's solution, ethyl alcohol, and mixtures thereof.

Exemplary lubricating agents include magnesium stearate, calciumstearate, stearic acid, silica, talc, malt, glyceryl behanate,hydrogenated vegetable oils, polyethylene glycol, sodium benzoate,sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate,sodium lauryl sulfate, and mixtures thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu,bergamot, black current seed, borage, cade, chamomile, canola, caraway,carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee,corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed,geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate,jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macadamianut, mallow, mango seed, meadow foam seed, mink, nutmeg, olive, orange,orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed,pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood,sasquana, savoury, sea buckthorn, sesame, shea butter, silicone,soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, andwheat germ oils. Exemplary synthetic oils include, but are not limitedto, butyl stearate, caprylic triglyceride, capric triglyceride,cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate,mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixturesthereof.

Liquid dosage forms for oral and parenteral administration includepharmaceutically acceptable emulsions, microemulsions, solutions,suspensions, syrups and elixirs. In addition to the active ingredients,the liquid dosage forms may comprise inert diluents commonly used in theart such as, for example, water or other solvents, solubilizing agentsand emulsifiers such as ethyl alcohol, isopropyl alcohol, ethylcarbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed,groundnut, corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can include adjuvants such as wetting agents, emulsifyingand suspending agents, sweetening, flavoring, and perfuming agents. Incertain embodiments for parenteral administration, the conjugatesdescribed herein are mixed with solubilizing agents such as Cremophor®,alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins,polymers, and mixtures thereof.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions can be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation can be a sterile injectable solution,suspension, or emulsion in a nontoxic parenterally acceptable diluent orsolvent, for example, as a solution in 1,3-butanediol. Among theacceptable vehicles and solvents that can be employed are water,Ringer's solution, U.S.P., and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or di-glycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium prior to use.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This can be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolution,which, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform may be accomplished by dissolving or suspending the drug in an oilvehicle.

Compositions for rectal or vaginal administration are typicallysuppositories which can be prepared by mixing the conjugates describedherein with suitable non-irritating excipients or carriers such as cocoabutter, polyethylene glycol, or a suppository wax which are solid atambient temperature but liquid at body temperature and therefore melt inthe rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets,pills, powders, and granules. In such solid dosage forms, the activeingredient is mixed with at least one inert, pharmaceutically acceptableexcipient or carrier such as sodium citrate or dicalcium phosphateand/or (a) fillers or extenders such as starches, lactose, sucrose,glucose, mannitol, and silicic acid, (b) binders such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone,sucrose, and acacia, (c) humectants such as glycerol, (d) disintegratingagents such as agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, (e) solutionretarding agents such as paraffin, (f) absorption accelerators such asquaternary ammonium compounds, (g) wetting agents such as, for example,cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolinand bentonite clay, and (i) lubricants such as talc, calcium stearate,magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate,and mixtures thereof. In the case of capsules, tablets, and pills, thedosage form may include a buffering agent.

Solid compositions of a similar type can be employed as fillers in softand hard-filled gelatin capsules using such excipients as lactose ormilk sugar as well as high molecular weight polyethylene glycols and thelike. The solid dosage forms of tablets, dragees, capsules, pills, andgranules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the art of pharmacology. Theymay optionally comprise opacifying agents and can be of a compositionthat they release the active ingredient(s) only, or preferentially, in acertain part of the intestinal tract, optionally, in a delayed manner.Examples of encapsulating compositions which can be used includepolymeric substances and waxes. Solid compositions of a similar type canbe employed as fillers in soft and hard-filled gelatin capsules usingsuch excipients as lactose or milk sugar as well as high molecularweight polyethylene glycols and the like.

The active ingredient can be in a micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings, and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active ingredient can be admixed with at least oneinert diluent such as sucrose, lactose, or starch. Such dosage forms maycomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may comprise bufferingagents. They may optionally comprise opacifying agents and can be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of encapsulating agents which can be usedinclude polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a compounddescribed herein may include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants, and/or patches. Generally, theactive ingredient is admixed under sterile conditions with apharmaceutically acceptable carrier or excipient and/or any neededpreservatives and/or buffers as can be required. Additionally, thepresent disclosure contemplates the use of transdermal patches, whichoften have the added advantage of providing controlled delivery of anactive ingredient to the body. Such dosage forms can be prepared, forexample, by dissolving and/or dispensing the active ingredient in theproper medium. Alternatively or additionally, the rate can be controlledby either providing a rate controlling membrane and/or by dispersing theactive ingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceuticalcompositions described herein include short needle devices. Intradermalcompositions can be administered by devices which limit the effectivepenetration length of a needle into the skin. Alternatively oradditionally, conventional syringes can be used in the classical mantouxmethod of intradermal administration. Jet injection devices whichdeliver liquid formulations to the dermis via a liquid jet injectorand/or via a needle which pierces the stratum corneum and produces a jetwhich reaches the dermis are suitable. Ballistic powder/particledelivery devices which use compressed gas to accelerate the compound inpowder form through the outer layers of the skin to the dermis aresuitable.

Formulations suitable for topical administration include, but are notlimited to, liquid and/or semi-liquid preparations such as liniments,lotions, oil-in-water and/or water-in-oil emulsions such as creams,ointments, and/or pastes, and/or solutions and/or suspensions. Topicallyadministrable formulations may, for example, comprise from about 1% toabout 10% (w/w) active ingredient, although the concentration of theactive ingredient can be as high as the solubility limit of the activeingredient in the solvent. Formulations for topical administration mayfurther comprise one or more of the additional ingredients describedherein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation suitable for pulmonary administration viathe buccal cavity. Such a formulation may comprise dry particles whichcomprise the active ingredient and which have a diameter in the rangefrom about 0.5 to about 7 nanometers, or from about 1 to about 6nanometers. Such compositions are conveniently in the form of drypowders for administration using a device comprising a dry powderreservoir to which a stream of propellant can be directed to dispersethe powder and/or using a self-propelling solvent/powder dispensingcontainer such as a device comprising the active ingredient dissolvedand/or suspended in a low-boiling propellant in a sealed container. Suchpowders comprise particles wherein at least 98% of the particles byweight have a diameter greater than 0.5 nanometers and at least 95% ofthe particles by number have a diameter less than 7 nanometers.Alternatively, at least 95% of the particles by weight have a diametergreater than 1 nanometer and at least 90% of the particles by numberhave a diameter less than 6 nanometers. Dry powder compositions mayinclude a solid fine powder diluent such as sugar and are convenientlyprovided in a unit dose form.

Low boiling propellants generally include liquid propellants having aboiling point of below 65° F. at atmospheric pressure. Generally thepropellant may constitute 50 to 99.9% (w/w) of the composition, and theactive ingredient may constitute 0.1 to 20% (w/w) of the composition.The propellant may further comprise additional ingredients such as aliquid non-ionic and/or solid anionic surfactant and/or a solid diluent(which may have a particle size of the same order as particlescomprising the active ingredient).

Pharmaceutical compositions described herein formulated for pulmonarydelivery may provide the active ingredient in the form of droplets of asolution and/or suspension. Such formulations can be prepared, packaged,and/or sold as aqueous and/or dilute alcoholic solutions and/orsuspensions, optionally sterile, comprising the active ingredient, andmay conveniently be administered using any nebulization and/oratomization device. Such formulations may further comprise one or moreadditional ingredients including, but not limited to, a flavoring agentsuch as saccharin sodium, a volatile oil, a buffering agent, a surfaceactive agent, and/or a preservative such as methylhydroxybenzoate. Thedroplets provided by this route of administration may have an averagediameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery areuseful for intranasal delivery of a pharmaceutical composition describedherein. Another formulation suitable for intranasal administration is acoarse powder comprising the active ingredient and having an averageparticle from about 0.2 to 500 micrometers. Such a formulation isadministered by rapid inhalation through the nasal passage from acontainer of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise fromabout as little as 0.1% (w/w) to as much as 100% (w/w) of the activeingredient, and may comprise one or more of the additional ingredientsdescribed herein. A pharmaceutical composition described herein can beprepared, packaged, and/or sold in a formulation for buccaladministration. Such formulations may, for example, be in the form oftablets and/or lozenges made using conventional methods, and maycontain, for example, 0.1 to 20% (w/w) active ingredient, the balancecomprising an orally dissolvable and/or degradable composition and,optionally, one or more of the additional ingredients described herein.Alternately, formulations for buccal administration may comprise apowder and/or an aerosolized and/or atomized solution and/or suspensioncomprising the active ingredient. Such powdered, aerosolized, and/oraerosolized formulations, when dispersed, may have an average particleand/or droplet size in the range from about 0.1 to about 200 nanometers,and may further comprise one or more of the additional ingredientsdescribed herein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation for ophthalmic administration. Suchformulations may, for example, be in the form of eye drops including,for example, a 0.1-1.0% (w/w) solution and/or suspension of the activeingredient in an aqueous or oily liquid carrier or excipient. Such dropsmay further comprise buffering agents, salts, and/or one or more otherof the additional ingredients described herein. Otherophthalmically-administrable formulations which are useful include thosewhich comprise the active ingredient in microcrystalline form and/or ina liposomal preparation. Ear drops and/or eye drops are alsocontemplated as being within the scope of this disclosure.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions which aresuitable for administration to humans, such compositions are generallysuitable for administration to animals of all sorts. Modification ofpharmaceutical compositions suitable for administration to humans inorder to render the compositions suitable for administration to variousanimals is well understood, and the ordinarily skilled veterinarypharmacologist can design and/or perform such modification with ordinaryexperimentation.

The compounds provided herein are typically formulated in dosage unitform for ease of administration and uniformity of dosage. It will beunderstood, however, that the total daily usage of the compositionsdescribed herein will be decided by a physician within the scope ofsound medical judgment. The specific therapeutically effective doselevel for any particular subject or organism will depend upon a varietyof factors including the disease being treated and the severity of thedisorder; the activity of the specific active ingredient employed; thespecific composition employed; the age, body weight, general health,sex, and diet of the subject; the time of administration, route ofadministration, and rate of excretion of the specific active ingredientemployed; the duration of the treatment; drugs used in combination orcoincidental with the specific active ingredient employed; and likefactors well known in the medical arts.

The compounds and compositions provided herein can be administered byany route, including enteral (e.g., oral), parenteral, intravenous,intramuscular, intra-arterial, intramedullary, intrathecal,subcutaneous, intraventricular, transdermal, interdermal, rectal,intravaginal, intraperitoneal, topical (as by powders, ointments,creams, and/or drops), mucosal, nasal, buccal, sublingual; byintratracheal instillation, bronchial instillation, and/or inhalation;and/or as an oral spray, nasal spray, and/or aerosol. Specificallycontemplated routes are oral administration, intravenous administration(e.g., systemic intravenous injection), regional administration viablood and/or lymph supply, and/or direct administration to an affectedsite. In general, the most appropriate route of administration willdepend upon a variety of factors including the nature of the agent(e.g., its stability in the environment of the gastrointestinal tract),and/or the condition of the subject (e.g., whether the subject is ableto tolerate oral administration). In certain embodiments, the compoundor pharmaceutical composition described herein is suitable for topicaladministration to the eye of a subject.

The exact amount of a compound required to achieve an effective amountwill vary from subject to subject, depending, for example, on species,age, and general condition of a subject, severity of the side effects ordisorder, identity of the particular compound, mode of administration,and the like. An effective amount may be included in a single dose(e.g., single oral dose) or multiple doses (e.g., multiple oral doses).In certain embodiments, when multiple doses are administered to asubject or applied to a biological sample, tissue, or cell, any twodoses of the multiple doses include different or substantially the sameamounts of a compound described herein. In certain embodiments, whenmultiple doses are administered to a subject or applied to a biologicalsample, tissue, or cell, the frequency of administering the multipledoses to the subject or applying the multiple doses to the tissue orcell is three doses a day, two doses a day, one dose a day, one doseevery other day, one dose every third day, one dose every week, one doseevery two weeks, one dose every three weeks, or one dose every fourweeks. In certain embodiments, the frequency of administering themultiple doses to the subject or applying the multiple doses to thetissue or cell is one dose per day. In certain embodiments, thefrequency of administering the multiple doses to the subject or applyingthe multiple doses to the tissue or cell is two doses per day. Incertain embodiments, the frequency of administering the multiple dosesto the subject or applying the multiple doses to the tissue or cell isthree doses per day. In certain embodiments, when multiple doses areadministered to a subject or applied to a biological sample, tissue, orcell, the duration between the first dose and last dose of the multipledoses is one day, two days, four days, one week, two weeks, three weeks,one month, two months, three months, four months, six months, ninemonths, one year, two years, three years, four years, five years, sevenyears, ten years, fifteen years, twenty years, or the lifetime of thesubject, biological sample, tissue, or cell. In certain embodiments, theduration between the first dose and last dose of the multiple doses isthree months, six months, or one year. In certain embodiments, theduration between the first dose and last dose of the multiple doses isthe lifetime of the subject, biological sample, tissue, or cell. Incertain embodiments, a dose (e.g., a single dose, or any dose ofmultiple doses) described herein includes independently between 0.1 μgand 1 μg, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg,between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg,between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive,of a compound described herein. In certain embodiments, a dose describedherein includes independently between 1 mg and 3 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 3 mg and 10 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 10 mg and 30 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 30 mg and 100 mg, inclusive, of acompound described herein.

In certain embodiments, an effective amount of a compound foradministration one or more times a day to a 70 kg adult human comprisesabout 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg,about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg toabout 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg,or about 100 mg to about 1000 mg, of a compound per unit dosage form.

In certain embodiments, the compound of the invention is administeredorally or parenterally at dosage levels sufficient to deliver from about0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg,preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg,from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1mg/kg to about 25 mg/kg, of subject body weight per day, one or moretimes a day, to obtain the desired therapeutic effect.

Dose ranges as described herein provide guidance for the administrationof provided pharmaceutical compositions to an adult. The amount to beadministered to, for example, a child or an adolescent can be determinedby a medical practitioner or person skilled in the art and can be loweror the same as that administered to an adult.

A compound or composition, as described herein, can be administered incombination with one or more additional pharmaceutical agents (e.g.,therapeutically and/or prophylactically active agents) useful intreating and/or preventing a proliferative disease. The compounds orcompositions can be administered in combination with additionalpharmaceutical agents that improve their activity (e.g., activity (e.g.,potency and/or efficacy) in treating a proliferative disease in asubject in need thereof, in preventing a proliferative disease in asubject in need thereof, and/or in inhibiting the activity of a proteinkinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject,biological sample, tissue, or cell), improve bioavailability, improvesafety, reduce drug resistance, reduce and/or modify metabolism, inhibitexcretion, and/or modify distribution in a subject, biological sample,tissue, or cell. It will also be appreciated that the therapy employedmay achieve a desired effect for the same disorder, and/or it mayachieve different effects. In certain embodiments, a pharmaceuticalcomposition described herein including a compound described herein andan additional pharmaceutical agent shows a synergistic effect that isabsent in a pharmaceutical composition including one of the compound andthe additional pharmaceutical agent, but not both.

The compound or composition can be administered concurrently with, priorto, or subsequent to one or more additional pharmaceutical agents, whichmay be useful as, e.g., combination therapies in treating and/orpreventing a proliferative disease. Pharmaceutical agents includetherapeutically active agents. Pharmaceutical agents also includeprophylactically active agents. Pharmaceutical agents include smallorganic molecules such as drug compounds (e.g., compounds approved forhuman or veterinary use by the U.S. Food and Drug Administration asprovided in the Code of Federal Regulations (CFR)), peptides, proteins,carbohydrates, monosaccharides, oligosaccharides, polysaccharides,nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides orproteins, small molecules linked to proteins, glycoproteins, steroids,nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides,antisense oligonucleotides, lipids, hormones, vitamins, and cells. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in treating a proliferative disease. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in preventing a proliferative disease. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in inhibiting the activity of a proteinkinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject,biological sample, tissue, or cell. In certain embodiments, theadditional pharmaceutical agent is a pharmaceutical agent useful ininducing apoptosis in a cell. In certain embodiments, the additionalpharmaceutical agent is a pharmaceutical agent approved by a regulatoryagency (e.g., the US FDA) for treating and/or preventing a proliferativedisease. Each additional pharmaceutical agent may be administered at adose and/or on a time schedule determined for that pharmaceutical agent.The additional pharmaceutical agent(s) may also be administered togetherwith each other and/or with the compound or composition described hereinin a single dose or administered separately in different doses. Theparticular combination to employ in a regimen will take into accountcompatibility of the compound described herein with the additionalpharmaceutical agent(s) and/or the desired therapeutic and/orprophylactic effect to be achieved. In general, it is expected that theadditional pharmaceutical agent(s) in combination be utilized at levelsthat do not exceed the levels at which they are utilized individually.In some embodiments, the levels utilized in combination will be lowerthan those utilized individually.

In certain embodiments, the additional pharmaceutical agent is ananti-proliferative agent (e.g., anti-cancer agent). In certainembodiments, the additional pharmaceutical agent is an anti-leukemiaagent. In certain embodiments, the additional pharmaceutical agent isABITREXATE (methotrexate), ADE, Adriamycin RDF (doxorubicinhydrochloride), Ambochlorin (chlorambucil), ARRANON (nelarabine),ARZERRA (ofatumumab), BOSULIF (bosutinib), BUSULFEX (busulfan), CAMPATH(alemtuzumab), CERUBIDINE (daunorubicin hydrochloride), CLAFEN(cyclophosphamide), CLOFAREX (clofarabine), CLOLAR (clofarabine), CVP,CYTOSAR-U (cytarabine), CYTOXAN (cyclophosphamide), ERWINAZE(Asparaginase Erwinia Chrysanthemi), FLUDARA (fludarabine phosphate),FOLEX (methotrexate), FOLEX PFS (methotrexate), GAZYVA (obinutuzumab),GLEEVEC (imatinib mesylate), Hyper-CVAD, ICLUSIG (ponatinibhydrochloride), IMBRUVICA (ibrutinib), LEUKERAN (chlorambucil),LINFOLIZIN (chlorambucil), MARQIBO (vincristine sulfate liposome),METHOTREXATE LPF (methorexate), MEXATE (methotrexate), MEXATE-AQ(methotrexate), mitoxantrone hydrochloride, MUSTARGEN (mechlorethaminehydrochloride), MYLERAN (busulfan), NEOSAR (cyclophosphamide), ONCASPAR(Pegaspargase), PURINETHOL (mercaptopurine), PURIXAN (mercaptopurine),Rubidomycin (daunorubicin hydrochloride), SPRYCEL (dasatinib), SYNRIBO(omacetaxine mepesuccinate), TARABINE PFS (cytarabine), TASIGNA(nilotinib), TREANDA (bendamustine hydrochloride), TRISENOX (arsenictrioxide), VINCASAR PFS (vincristine sulfate), ZYDELIG (idelalisib), ora combination thereof. In certain embodiments, the additionalpharmaceutical agent is an anti-lymphoma agent. In certain embodiments,the additional pharmaceutical agent is ABITREXATE (methotrexate), ABVD,ABVE, ABVE-PC, ADCETRIS (brentuximab vedotin), ADRIAMYCIN PFS(doxorubicin hydrochloride), ADRIAMYCIN RDF (doxorubicin hydrochloride),AMBOCHLORIN (chlorambucil), AMBOCLORIN (chlorambucil), ARRANON(nelarabine), BEACOPP, BECENUM (carmustine), BELEODAQ (belinostat),BEXXAR (tositumomab and iodine I 131 tositumomab), BICNU (carmustine),BLENOXANE (bleomycin), CARMUBRIS (carmustine), CHOP, CLAFEN(cyclophosphamide), COPP, COPP-ABV, CVP, CYTOXAN (cyclophosphamide),DEPOCYT (liposomal cytarabine), DTIC-DOME (dacarbazine), EPOCH, FOLEX(methotrexate), FOLEX PFS (methotrexate), FOLOTYN (pralatrexate),HYPER-CVAD, ICE, IMBRUVICA (ibrutinib), INTRON A (recombinant interferonalfa-2b), ISTODAX (romidepsin), LEUKERAN (chlorambucil), LINFOLIZIN(chlorambucil), Lomustine, MATULANE (procarbazine hydrochloride),METHOTREXATE LPF (methotrexate), MEXATE (methotrexate), MEXATE-AQ(methotrexate), MOPP, MOZOBIL (plerixafor), MUSTARGEN (mechlorethaminehydrochloride), NEOSAR (cyclophosphamide), OEPA, ONTAK (denileukindiftitox), OPPA, R-CHOP, REVLIMID (lenalidomide), RITUXAN (rituximab),STANFORD V, TREANDA (bendamustine hydrochloride), VAMP, VELBAN(vinblastine sulfate), VELCADE (bortezomib), VELSAR (vinblastinesulfate), VINCASAR PFS (vincristine sulfate), ZEVALIN (ibritumomabtiuxetan), ZOLINZA (vorinostat), ZYDELIG (idelalisib), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isan anti-myelodysplasia agent. In certain embodiments, the additionalpharmaceutical agent is REVLIMID (lenalidomide), DACOGEN (decitabine),VIDAZA (azacitidine), CYTOSAR-U (cytarabine), IDAMYCIN (idarubicin),CERUBIDINE (daunorubicin), or a combination thereof.

In certain embodiments, the additional pharmaceutical agent is ananti-macroglobulinemia agent. In certain embodiments, the additionalpharmaceutical agent is LEUKERAN (chlorambucil), NEOSAR(cyclophosphamide), FLUDARA (fludarabine), LEUSTATIN (cladribine), or acombination thereof. In certain embodiments, the additionalpharmaceutical agent is ABITREXATE (methotrexate), ABRAXANE (paclitaxelalbumin-stabilized nanoparticle formulation), AC, AC-T, ADE, ADRIAMYCINPFS (doxorubicin hydrochloride), ADRUCIL (fluorouracil), AFINITOR(everolimus), AFINITOR DISPERZ (everolimus), ALDARA (imiquimod), ALIMTA(pemetrexed disodium), AREDIA (pamidronate disodium), ARIMIDEX(anastrozole), AROMASIN (exemestane), AVASTIN (bevacizumab), BECENUM(carmustine), BEP, BICNU (carmustine), BLENOXANE (bleomycin), CAF,CAMPTOSAR (irinotecan hydrochloride), CAPDX, CAPRELSA (vandetanib),CARBOPLATIN-TAXOL, CARMUBRIS (carmustine), CAS ODEX (bicalutamide),CEENU (lomustine), CERUBIDINE (daunorubicin hydrochloride), CERVARIX(recombinant HPV bivalent vaccine), CLAFEN (cyclophosphamide), CMF,COMETRIQ (cabozantinib-s-malate), COSMEGEN (dactinomycin), CYFOS(ifosfamide), CYRAMZA (ramucirumab), CYTOSAR-U (cytarabine), CYTOXAN(cyclophosphamide), DACOGEN (decitabine), DEGARELIX, DOXIL (doxorubicinhydrochloride liposome), DOXORUBICIN HYDROCHLORIDE, DOX-SL (doxorubicinhydrochloride liposome), DTIC-DOME (dacarbazine), EFUDEX (fluorouracil),ELLENCE (epirubicin hydrochloride), ELOXATIN (oxaliplatin), ERBITUX(cetuximab), ERIVEDGE (vismodegib), ETOPOPHOS (etoposide phosphate),EVACET (doxorubicin hydrochloride liposome), FARES TON (toremifene), FASLODEX (fulvestrant), FEC, FEMARA (letrozole), FLUOROPLEX (fluorouracil),FOLEX (methotrexate), FOLEX PFS (methotrexate), FOLFIRI,FOLFIRI-BEVACIZUMAB, FOLFIRI-CETUXIMAB, FOLFIRINOX, FOLFOX, FU-LV,GARDASIL (recombinant human papillomavirus (HPV) quadrivalent vaccine),GEMCITABINE-CISPLATIN, GEMCITABINE-OXALIPLATIN, GEMZAR (gemcitabinehydrochloride), GILOTRIF (afatinib dimaleate), GLEEVEC (imatinibmesylate), GLIADEL (carmustine implant), GLIADEL WAFER (carmustineimplant), HERCEPTIN (trastuzumab), HYCAMTIN (topotecan hydrochloride),IFEX (ifosfamide), IFOSFAMIDUM (ifosfamide), INLYTA (axitinib), INTRON A(recombinant interferon alfa-2b), IRESS A (gefitinib), IXEMPRA(ixabepilone), JAKAFI (ruxolitinib phosphate), JEVTANA (cabazitaxel),KADCYLA (ado-trastuzumab emtansine), KEYTRUDA (pembrolizumab), KYPROLIS(carfilzomib), LIPODOX (doxorubicin hydrochloride liposome), LUPRON(leuprolide acetate), LUPRON DEPOT (leuprolide acetate), LUPRON DEPOT-3MONTH (leuprolide acetate), LUPRON DEPOT-4 MONTH (leuprolide acetate),LUPRON DEPOT-PED (leuprolide acetate), MEGACE (megestrol acetate),MEKINIST (trametinib), METHAZOLAS TONE (temozolomide), METHOTREXATE LPF(methotrexate), MEXATE (methotrexate), MEXATE-AQ (methotrexate),MITOXANTRONE HYDROCHLORIDE, MITOZYTREX (mitomycin c), MOZOBIL(plerixafor), MUSTARGEN (mechlorethamine hydrochloride), MUTAMYCIN(mitomycin c), MYLOSAR (azacitidine), NAVELBINE (vinorelbine tartrate),NEOSAR (cyclophosphamide), NEXAVAR (sorafenib tosylate), NOLVADEX(tamoxifen citrate), NOVALDEX (tamoxifen citrate), OFF, PAD, PARAPLAT(carboplatin), PARAPLATIN (carboplatin), PEG-INTRON (peginterferonalfa-2b), PEMETREXED DISODIUM, PERJETA (pertuzumab), PLATINOL(cisplatin), PLATINOL-AQ (cisplatin), POMALYST (pomalidomide),prednisone, PROLEUKIN (aldesleukin), PROLIA (denosumab), PROVENGE(sipuleucel-t), REVLIMID (lenalidomide), RUBIDOMYCIN (daunorubicinhydrochloride), SPRYCEL (dasatinib), STIVARGA (regorafenib), SUTENT(sunitinib malate), SYLATRON (peginterferon alfa-2b), SYLVANT(siltuximab), SYNOVIR (thalidomide), TAC, TAFINLAR (dabrafenib),TARABINE PFS (cytarabine), TARCEVA (erlotinib hydrochloride), TASIGNA(nilotinib), TAXOL (paclitaxel), TAXOTERE (docetaxel), TEMODAR(temozolomide), THALOMID (thalidomide), TOPOSAR (etoposide), TORISEL(temsirolimus), TPF, TRISENOX (arsenic trioxide), TYKERB (lapatinibditosylate), VECTIBIX (panitumumab), VEIP, VELBAN (vinblastine sulfate),VELCADE (bortezomib), VELSAR (vinblastine sulfate), VEPESID (etoposide),VIADUR (leuprolide acetate), VIDAZA (azacitidine), VINCASAR PFS(vincristine sulfate), VOTRIENT (pazopanib hydrochloride), WELLCOVORIN(leucovorin calcium), XALKORI (crizotinib), XELODA (capecitabine),XELOX, XGEVA (denosumab), XOFIGO (radium 223 dichloride), XTANDI(enzalutamide), YERVOY (ipilimumab), ZALTRAP (ziv-aflibercept), ZELBORAF(vemurafenib), ZOLADEX (goserelin acetate), ZOMETA (zoledronic acid),ZYKADIA (ceritinib), ZYTIGA (abiraterone acetate), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isa protein kinase inhibitor (e.g., tyrosine protein kinase inhibitor). Incertain embodiments, the additional pharmaceutical agent is an inhibitorof a Src family kinase. In certain embodiments, the additionalpharmaceutical agent is a CDK inhibitor. In certain embodiments, theadditional pharmaceutical agent is a CDK7 inhibitor. In certainembodiments, the additional pharmaceutical agent is a CDK12 inhibitor.In certain embodiments, the additional pharmaceutical agent is a CDK13inhibitor. In certain embodiments, the additional pharmaceutical agentis an inhibitor of one or more protein kinases selected from the groupconsisting of IRAK1, IRAK4, BMX, and PI3K. In certain embodiments, theadditional pharmaceutical agent is an inhibitor of one or more proteinkinases selected from the group consisting of BUB1B, CDK2, CDK9, CHEK2,FGR, HIPK4, PRKCQ, RET, SRC, or MELK. In certain embodiments, theadditional pharmaceutical agent is an inhibitor of one or more proteinkinases selected from the group consisting of ABL, ARG, BLK, CSK, EphB1,EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, andTEC. In certain embodiments, the additional pharmaceutical agent is aninhibitor of one or more protein kinases selected from the groupconsisting of ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK,EPHA4, EPHB2, EPHB3, EPHB4, FGR, JAK3(JH1domain-catalytic), KIT,KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated,ABL1(Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN,ABL1(Q252H)-nonphosphorylated, DDR¹, EPHB1, ERBB4, p38-alpha, ABL2,ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5,ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK,EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q), ERBB2,ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del, A750P),CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR,KIT-autoinhibited, and EGFR(E746-A750del). In certain embodiments, theadditional pharmaceutical agent is an inhibitor of one or more proteinkinases selected from the group consisting ofABL1(F317L)-nonphosphorylated, ABL1(H396P)-nonphosphorylated,ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2,EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D),LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated,ABL1(Y253F)-phosphorylated, ERBB3, FGR, FRK, p38-alpha,ABL1(F317I)-nonphosphorylated, DDR¹, EPHA2, ABL1(Q252H)-phosphorylated,MEK5, ABL1(Q252H)-nonphosphorylated, ABL2, FYN, EPHB1,ABL1(E255K)-phosphorylated, ABL1(F317L)-phosphorylated, EPHA1,ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5,EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V),KIT-autoinhibited, EGFR(L747-T751del,Sins), EGFR(L858R),EGFR(L747-E749del, A750P), and CSF1R. In certain embodiments, theadditional pharmaceutical agent is an anti-angiogenesis agent,anti-inflammatory agent, immunosuppressant, anti-bacterial agent,anti-viral agent, cardiovascular agent, cholesterol-lowering agent,anti-diabetic agent, anti-allergic agent, pain-relieving agent, or acombination thereof. In certain embodiments, the compounds describedherein or pharmaceutical compositions can be administered in combinationwith an anti-cancer therapy including, but not limited to,transplantation (e.g., bone marrow transplantation, stem celltransplantation), surgery, radiation therapy, immunotherapy, andchemotherapy.

Also encompassed by the disclosure are kits (e.g., pharmaceuticalpacks). The kits provided may comprise a pharmaceutical composition orcompound described herein and a container (e.g., a vial, ampule, bottle,syringe, and/or dispenser package, or other suitable container). In someembodiments, provided kits may optionally further include a secondcontainer comprising a pharmaceutical excipient for dilution orsuspension of a pharmaceutical composition or compound described herein.In some embodiments, the pharmaceutical composition or compounddescribed herein provided in the first container and the secondcontainer are combined to form one unit dosage form.

In certain embodiments, a kit described herein includes a firstcontainer comprising a compound or pharmaceutical composition describedherein. In certain embodiments, a kit described herein is useful intreating a proliferative disease (e.g., cancers (e.g., leukemia, acutelymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiplemyeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer,neuroblastoma, lung cancer, colorectal cancer), benign neoplasms,diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases) in a subject in needthereof, preventing a proliferative disease in a subject in needthereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g.,CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue, orcell, and/or inducing apoptosis in a cell.

In certain embodiments, a kit described herein further includesinstructions for using the compound or pharmaceutical compositionincluded in the kit. A kit described herein may also include informationas required by a regulatory agency such as the U.S. Food and DrugAdministration (FDA). In certain embodiments, the information includedin the kits is prescribing information. In certain embodiments, the kitsand instructions provide for treating a proliferative disease in asubject in need thereof, preventing a proliferative disease in a subjectin need thereof, inhibiting the activity of a protein kinase (e.g., CDK(e.g., CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue,or cell, and/or inducing apoptosis in a cell. A kit described herein mayinclude one or more additional pharmaceutical agents described herein asa separate composition.

Methods of Treatment and Uses

The present invention also provides methods for the treatment orprevention of a proliferative disease (e.g., cancers (e.g., leukemia,acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma,multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, braincancer, neuroblastoma, lung cancer, colorectal cancer), benignneoplasms, diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases).

The compounds described herein may exhibit kinase inhibitory activity;the ability to inhibit cyclin-dependent kinase (CDK); the ability toinhibit cyclin-dependent kinase 7 (CDK7); the ability to inhibitcyclin-dependent kinase 7 (CDK7), without inhibiting anothercyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependentkinase 12 (CDK12); the ability to inhibit cyclin-dependent kinase 12(CDK12), without inhibiting another cyclin-dependent kinase (CDK); theability to inhibit cyclin-dependent kinase 13 (CDK13); the ability toinhibit cyclin-dependent kinase 13 (CDK13), without inhibiting anothercyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependentkinases 12 and 13 (CDK12 and CDK13); the ability to inhibitcyclin-dependent kinases 12 and 13 (CDK12 and CDK13), without inhibitinganother cyclin-dependent kinase (CDK); a therapeutic effect and/orpreventative effect in the treatment of cancers; a therapeutic effectand/or preventative effect in the treatment of Myc-dependent cancers;and/or a therapeutic profile (e.g., optimum safety and curative effect)that is superior to existing chemotherapeutic agents.

Without wishing to be bound by any particular theory, the compoundsdescribed herein are able to bind (e.g., covalently modify) a proteinkinase described herein. In certain embodiments, the R² group of acompound described herein is able to bind (e.g., covalently modify) tothe protein kinase. In certain embodiments, the R² group of a compounddescribed herein is able to covalently bind a cysteine residue of theprotein kinase. In certain embodiments, the R² group of a compounddescribed herein is able to covalently bind Cys312 residue of CDK7. Incertain embodiments, the R² group of a compound described herein is ableto covalently bind Cys Cys1039 residue of CDK12. In certain embodiments,the R² group of a compound described herein is able to covalently bindCys1017 residue of CDK13.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a subject, the methods comprisingadministering to the subject an effective amount (e.g., therapeuticallyeffective amount) of a compound, or pharmaceutical composition thereof,as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a biological sample, the methodscomprising contacting the biological sample with an effective amount ofa compound, or pharmaceutical composition thereof, as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a tissue, the methods comprisingcontacting the tissue with an effective amount of a compound, orpharmaceutical composition thereof, as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a cell, the methods comprisingcontacting the cell with an effective amount of a compound, orpharmaceutical composition thereof, as described herein.

In certain embodiments, the subject being treated is a mammal. Incertain embodiments, the subject is a human. In certain embodiments, thesubject is a domesticated animal, such as a dog, cat, cow, pig, horse,sheep, or goat. In certain embodiments, the subject is a companionanimal such as a dog or cat. In certain embodiments, the subject is alivestock animal such as a cow, pig, horse, sheep, or goat. In certainembodiments, the subject is a zoo animal. In another embodiment, thesubject is a research animal such as a rodent, dog, or non-humanprimate. In certain embodiments, the subject is a non-human transgenicanimal such as a transgenic mouse or transgenic pig.

In certain embodiments, a biological sample described herein is a breasttissue, bone marrow, lymph node, spleen, or blood.

In certain embodiments, a cell described herein is in vitro. In certainembodiments, a cell described herein is ex vivo. In certain embodiments,a cell described herein is in vivo. In certain embodiments, a celldescribed herein is a malignant cell (e.g., malignant blood cell). Incertain embodiments, a cell described herein is a malignanthematopoietic stem cell (e.g., malignant myeloid cell or malignantlymphoid cell). In certain embodiments, a cell described herein is amalignant lymphocyte (e.g., malignant T-cell or malignant B-cell). Incertain embodiments, a cell described herein is a malignant red bloodcell, malignant white blood cell, or malignant platelet. In certainembodiments, a cell described herein is a malignant neutrophil,malignant macrophage, or malignant plasma cell. In certain embodiments,a cell described herein is a carcinoma cell. In certain embodiments, acell described herein is a carcinoma breast cell. In certainembodiments, a cell described herein is a sarcomas cell. In certainembodiments, a cell described herein is a sarcomas breast cell.

The proliferative disease to be treated or prevented using the compoundsdescribed herein may be associated with overexpression of a kinase, suchas cyclin-dependent kinase (CDK). The process of eukaryotic celldivision may be broadly divided into a series of sequential phasestermed G1, S, G2, and M. Correct progression through the various phasesof the cell cycle has been shown to be critically dependent upon thespatial and temporal regulation of a family of proteins known as cyclindependent kinases (CDKs) and a diverse set of their cognate proteinpartners termed cyclins. CDKs are CDC2 (also known as CDK1) homologousserine-threonine kinase proteins that are able to utilize ATP as asubstrate in the phosphorylation of diverse polypeptides in asequence-dependent context. Cyclins are a family of proteinscharacterized by a homology region, containing approximately 100 aminoacids, termed the “cyclin box” which is used in binding to, and definingselectivity for, specific CDK partner proteins.

Modulation of the expression levels, degradation rates, protein levels,and activity levels of various CDKs and cyclins throughout the cellcycle leads to the cyclical formation of a series of CDK/cyclincomplexes, in which the CDKs are enzymatically active. The formation ofthese complexes controls passage through discrete cell cycle checkpointsand thereby enables the process of cell division to continue. Failure tosatisfy the prerequisite biochemical criteria at a given cell cyclecheckpoint, i.e., failure to form a required CDK/cyclin complex, canlead to cell cycle arrest and/or cellular apoptosis. Aberrant cellularproliferation can often be attributed to loss of correct cell cyclecontrol. Inhibition of CDK enzymatic activity therefore provides a meansby which abnormally dividing cells can have their division arrestedand/or be killed. The diversity of CDKs, and CDK complexes, and theircritical roles in mediating the cell cycle, provides a broad spectrum ofpotential therapeutic targets selected on the basis of a definedbiochemical rationale.

CDK7, a member of the CDK family, was originally isolated as thecatalytic subunit of the trimeric CDK-activating kinase (CAK) complex.This complex, consisting of CDK7, cyclin H, and MAT1, is responsible foractivation of the mitotic promoting factor in vitro. The discovery thatCDK7 was also a component of the basal transcription repair factor IIH(TFIIH) implicated a dual role for CDK7 in transcription as part ofTFIIH and in the control of the cell cycle as the trimeric CAK complex.TFIIH is a multi-subunit protein complex identified as a factor requiredfor RNA polymerase II (RNAP II)-catalyzed transcription, andsubsequently this complex was found to play a key role in nucleotideexcision repair. CDK7 is a component of at least three complexes, i.e.,the trimeric CAK complex, the quaternary complex with the XPD (or ERCC2,a protein involved in transcription-coupled nucleotide excision repair),and the nine-subunit TFIIH complex. The two functions of CDK7 in CAK andCTD phosphorylation support critical facets of cellular proliferation,cell cycling, and transcription. Overexpression of CDK7 may inhibitapoptosis, promote transcription and cell proliferation, and/or disruptDNA repair, and therefore, cause proliferative diseases. In certainembodiments, the proliferative disease to be treated or prevented usingthe compounds described herein may be associated with overexpression ofa CDK (e.g., CDK7).

Cdk12 and Cdk13 are Cdc2-related proteins that share 92% identity intheir kinase domains (Chen et al., Exp. Neurol., 2014, 261, 10-21).CDK12 plays a critical role in cell processes, for example, regulatingtranscription and splicing machinery by stabilizing the RNAPII and DNAinteraction, and regulating DNA damage response (DDR) and maintenance ofgenomic stability by modulating the expression of DDR genes.Overexpression of CDK12 has been found to correlate, both at thetranscriptional and protein level, with pathological parameters ofbreast cancer disease.

A proliferative disease may be associated with aberrant activity of aCDK (e.g., CDK7, CDK12, and/or CDK13). Aberrant activity of a CDK (e.g.,CDK7, CDK12, and/or CDK13) may be an elevated and/or an inappropriateactivity of the CDK. Deregulation of cell cycle progression is acharacteristic of a proliferative disease, and a majority ofproliferative diseases have abnormalities in some component of CDK(e.g., CDK7, CDK12, and/or CDK13) activity, frequently through elevatedand/or inappropriate CDK activation. Inhibition of the catalyticactivity of CDK7, CDK12, and/or CDK13 would be expected to inhibit cellcycle progression by blocking the phosphorylation of cell cycle CDKs,and would additionally inhibit transcription of effectors of celldivision. In certain embodiments, CDK7 is not overexpressed, and theactivity of CDK7 is elevated and/or inappropriate. In certain otherembodiments, CDK7 is overexpressed, and the activity of CDK7 is elevatedand/or inappropriate. In certain embodiments, CDK12 is notoverexpressed, and the activity of CDK12 is elevated and/orinappropriate. In certain embodiments, CDK12 is overexpressed, and theactivity of CDK12 is elevated and/or inappropriate. In certain otherembodiments, CDK13 is not overexpressed, and the activity of CDK13 iselevated and/or inappropriate. In certain other embodiments, CDK13 isoverexpressed, and the activity of CDK13 is elevated and/orinappropriate. The compounds described herein, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, prodrugs,and compositions thereof, may inhibit the activity of CDK7 and be usefulin treating and/or preventing proliferative diseases. The compoundsdescribed herein, and pharmaceutically acceptable salts, solvates,hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, and compositions thereof,may inhibit the activity of CDK12 and/or CDK13 and be useful in treatingand/or preventing proliferative diseases.

A proliferative disease may also be associated with inhibition ofapoptosis of a cell in a biological sample or subject. All types ofbiological samples described herein or known in the art are contemplatedas being within the scope of the invention. Apoptosis is the process ofprogrammed cell death. Inhibition of apoptosis may result inuncontrolled cell proliferation and, therefore, may cause proliferativediseases. The cell cycle CDKs (CDK1, 2, 4, and 6) are activated byphosphorylation by CDK7/cyclin H (also called CAK). Inhibition of CDK7would therefore result in cell-cycle arrest at multiple points in thecell cycle due to failure to activate the cell cycle CDKs. CDK 7activates transcription by phosphorylating the CTD of RNAP II.Inhibition of CTD phosphorylation has been shown to inhibittranscription and reduce expression of short lived proteins, includingthose involved in apoptosis regulation. It is appreciated in the artthat stalling of RNA polymerase may activate p53 (also known as protein53 or tumor protein 53, a tumor suppressor protein that is encoded inhumans by the TP53 gene), leading to apoptosis. Thus, inhibition of theactivity of CDK7 are expected to cause cytotoxicity by inducingapoptosis. The compounds described herein, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, prodrugs,and compositions thereof, may induce apoptosis, and therefore, be usefulin treating and/or preventing proliferative diseases.

The CycK/Cdk12 complex regulates phosphorylation of Ser2 in theC-terminal domain of RNA polymerase II and expression of a small subsetof human genes, as revealed in expression microarrays. Throughregulation of expression of DNA damage response genes (i.e. oncogenes),CycK/Cdk12 protects cells from genomic instability. In certainembodiments, the DNA damage response genes are BRCA1, BRCA2, HER1, HER2,ATR, FANC1, or FANCD2. In certain embodiments, the DNA damage responsegenes are BRCA1, HER2, ATR, FANC1, and FANCD2. In certain embodiments,the DNA damage response genes are BRCA1. In certain embodiments, the DNAdamage response genes are HER2.

In certain embodiments, the proliferative disease to be treated orprevented using the compounds described herein is cancer. All types ofcancers disclosed herein or known in the art are contemplated as beingwithin the scope of the invention. In certain embodiments, theproliferative disease is a cancer associated with dependence on BCL-2anti-apoptotic proteins (e.g., MCL-1 and/or XIAP). In certainembodiments, the proliferative disease is a cancer associated withdependence on BCL-2 anti-apoptotic proteins (e.g., MCL-1 and/or XIAP).In certain embodiments, the proliferative disease is a cancer associatedwith overexpression of MYC (a gene that codes for a transcriptionfactor). In certain embodiments, the cancer is a MYC-dependent cancer.In certain embodiments, the proliferative disease is a cancer associatedwith amplification of BRCA1. In certain embodiments, the proliferativedisease is a cancer associated with amplification of HER2. In certainembodiments, the proliferative disease is a hematological malignancy. Incertain embodiments, the proliferative disease is a blood cancer. Incertain embodiments, the proliferative disease is a hematologicalmalignancy. In certain embodiments, the proliferative disease isleukemia. In certain embodiments, the proliferative disease is chroniclymphocytic leukemia (CLL). In certain embodiments, the proliferativedisease is acute lymphoblastic leukemia (ALL). In certain embodiments,the proliferative disease is T-cell acute lymphoblastic leukemia(T-ALL). In certain embodiments, the proliferative disease is chronicmyelogenous leukemia (CML). In certain embodiments, the proliferativedisease is acute myelogenous leukemia (AML). In certain embodiments, theproliferative disease is acute monocytic leukemia (AMoL). In certainembodiments, the proliferative disease is lymphoma. In some embodiments,the proliferative disease is Burkitt's lymphoma. In certain embodiments,the proliferative disease is a Hodgkin's lymphoma. In certainembodiments, the proliferative disease is a non-Hodgkin's lymphoma. Incertain embodiments, the proliferative disease is multiple myeloma. Incertain embodiments, the proliferative disease is melanoma. In certainembodiments, the proliferative disease is colorectal cancer. In certainembodiments, the proliferative disease is breast cancer. In certainembodiments, the proliferative disease is recurring breast cancer. Incertain embodiments, the proliferative disease is mutant breast cancer.In certain embodiments, the proliferative disease is HER2+ breastcancer. In certain embodiments, the proliferative disease is HER2−breast cancer. In certain embodiments, the proliferative disease istriple-negative breast cancer (TNBC). In certain embodiments, theproliferative disease is a bone cancer. In certain embodiments, theproliferative disease is osteosarcoma. In certain embodiments, theproliferative disease is Ewing's sarcoma. In some embodiments, theproliferative disease is a brain cancer. In some embodiments, theproliferative disease is neuroblastoma. In some embodiments, theproliferative disease is a lung cancer. In some embodiments, theproliferative disease is small cell lung cancer (SCLC). In someembodiments, the proliferative disease is non-small cell lung cancer. Insome embodiments, the proliferative disease is a benign neoplasm. Alltypes of benign neoplasms disclosed herein or known in the art arecontemplated as being within the scope of the invention. In someembodiments, the proliferative disease is associated with angiogenesis.All types of angiogenesis disclosed herein or known in the art arecontemplated as being within the scope of the invention. In certainembodiments, the proliferative disease is an inflammatory disease. Alltypes of inflammatory diseases disclosed herein or known in the art arecontemplated as being within the scope of the invention. In certainembodiments, the inflammatory disease is rheumatoid arthritis. Incertain embodiments, the proliferative disease is an acute inflammatorydisease. In certain embodiments, the acute inflammatory disease isrheumatoid arthritis, Crohn's disease, or fibrosis. In some embodiments,the proliferative disease is an autoinflammatory disease. All types ofautoinflammatory diseases disclosed herein or known in the art arecontemplated as being within the scope of the invention. In someembodiments, the proliferative disease is an autoimmune disease. Alltypes of autoimmune diseases disclosed herein or known in the art arecontemplated as being within the scope of the invention.

Another aspect of the invention relates to methods of inhibiting theactivity of a kinase in a biological sample or subject. In certainembodiments, the kinase is CDK. In certain embodiments, the kinase isCDK7. In certain embodiments, the kinase is CDK12. In certainembodiments, the kinase is CDK13. In certain embodiments, the activityof the kinase is aberrant activity of the kinase. In certainembodiments, the inhibition of the activity of the kinase isirreversible. In other embodiments, the inhibition of the activity ofthe kinase is reversible. In certain embodiments, the methods ofinhibiting the activity of the kinase include attaching a compounddescribed herein to the kinase.

Also provided in the present invention are methods of inhibitingtranscription of genes in a biological sample or subject. In certainembodiments, the genes which may have their transcription inhibited bythe activity of CDK7, CDK12, and/or CDK13 are listed in FIG. 11. Incertain embodiments, the transcription of genes affected by the activityof CDK7 may be inhibited by a compound of the invention. In certainembodiments, the genes which may have their transcription inhibited bythe activity of CDK7 are one or more selected from the group consistingof MYC, RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1,NEUROD1, NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B,PLK2, TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, and FOS1. In certainembodiments, the genes which may have their transcription inhibited bythe activity of CDK7 include MYC, KLF2, E2F2, CDK6, CCND3, E2F3, HNRPDL,TET1, IL7R, BRCA1, BRCA2, HER1, and HER2. In certain embodiments, thetranscription of genes affected by the activity of CDK12 may beinhibited by a compound of the invention. In certain embodiments, thegenes which may have their transcription inhibited by the activity ofCDK12 are one or more selected from the group consisting of BRCA1,FANC1, ATR, FANCD2, APEX1, NEK9, CHEK1, CHEK2, ATM, RAD51C, RAD51D,ORC3L, MDC1, TERF2, ERCC4, FANCF, PARP9, RUNX1, MYB, TAL1, MCL1, MYC,BCL2, ETS1, and EWS-FLI. In certain embodiments, the transcription ofgenes affected by the activity of CDK13 may be inhibited by a compoundof the invention. In certain embodiments, the genes which may have theirtranscription inhibited by the compounds herein are SNORA38.

The present invention also provides methods of inhibiting cell growth ina biological sample or subject.

In still another aspect, the present invention provides methods ofinducing apoptosis of a cell in a biological sample or a subject.

In certain embodiments, the methods described herein includeadministering to a subject or contacting a biological sample with aneffective amount of a compound described herein, or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, or apharmaceutical composition thereof. In certain embodiments, the methodsdescribed herein include administering to a subject or contacting abiological sample with an effective amount of a compound describedherein, or a pharmaceutically acceptable salt thereof, or apharmaceutical composition thereof. In certain embodiments, the compoundis contacted with a biological sample. In certain embodiments, thecompound is administered to a subject. In certain embodiments, thecompound is administered in combination with one or more additionalpharmaceutical agents described herein. The additional pharmaceuticalagent may be an anti-proliferative agent. In certain embodiments, theadditional pharmaceutical agent is an anti-cancer agent. The additionalpharmaceutical agent may also be a kinase inhibitor. In certainembodiments, the additional pharmaceutical agent is an inhibitor of aCDK. In certain embodiments, the additional pharmaceutical agent is aninhibitor of CDK7. In certain embodiments, the additional pharmaceuticalagent is a selective inhibitor of CDK7. In certain embodiments, theadditional pharmaceutical agent is a nonselective inhibitor of CDK7. Incertain embodiments, the additional pharmaceutical agent is an inhibitorof CDK12. In certain embodiments, the additional pharmaceutical agent isa selective inhibitor of CDK12. In certain embodiments, the additionalpharmaceutical agent is a nonselective inhibitor of CDK12. In certainembodiments, the additional pharmaceutical agent is an inhibitor ofCDK13. In certain embodiments, the additional pharmaceutical agent is aselective inhibitor of CDK13. In certain embodiments, the additionalpharmaceutical agent is a nonselective inhibitor of CDK13. In certainembodiments, the additional pharmaceutical agent is an inhibitor ofanother CDK. In certain embodiments, the additional pharmaceutical agentis a selective inhibitor of another CDK. In certain embodiments, theadditional pharmaceutical agent is a nonselective inhibitor of anotherCDK. In certain embodiments, the additional pharmaceutical agent isflavopiridol, triptolide, SNS-032 (BMS-387032), PHA-767491, PHA-793887,BS-181, (S)—CR⁸, (R)—CR⁸, or NU6140. In certain embodiments, theadditional pharmaceutical agent is an inhibitor of a mitogen-activatedprotein kinase (MAPK). In certain embodiments, the additionalpharmaceutical agent is an inhibitor of a glycogen synthase kinase 3(GSK3). In certain embodiments, the additional pharmaceutical agent isan inhibitor of an AGC kinase. In certain embodiments, the additionalpharmaceutical agent is an inhibitor of a calmodulin-dependent kinase(CaM Kinase). In certain embodiments, the additional pharmaceuticalagent is an inhibitor of a casein kinase 1. In certain embodiments, theadditional pharmaceutical agent is an inhibitor of a STE kinase. Incertain embodiments, the additional pharmaceutical agent is an inhibitorof a tyrosine kinase.

In some embodiments, the additional pharmaceutical agent is atopoisomerase inhibitor, a MCL1 inhibitor, a BCL-2 inhibitor, a BCL-xLinhibitor, a BRD4 inhibitor, a BRCA1 inhibitor, BRCA2 inhibitor, HER1inhibitor, HER2 inhibitor, a CDK9 inhibitor, a Jumonji histonedemethylase inhibitor, or a DNA damage inducer. In some embodiments, theadditional pharmaceutical agent is etoposide, obatoclax, navitoclax,JQ1,4-(((5′-chloro-2′-(((1R,4R)-4-(((R)-1-methoxypropan-2-yl)amino)cyclohexyl)amino)-[2,4′-bipyridin]-6-yl)amino)methyl)tetrahydro-2H-pyran-4-carbonitrile,JIB04, or cisplatin. In some embodiments, the additional pharmaceuticalagent is etoposide, obatoclax, or navitoclax, and the disease to betreated is breast cancer, e.g., triple-negative breast cancer, HER2positive breast cancer, HER2 negative breast cancer, ER-positive breastcancer, ER-negative breast cancer, or ER/PR-positive breast cancer. Insome embodiments, the additional pharmaceutical agent is etoposide,JIB04, or cisplatin, and the disease to be treated is Ewing's sarcoma.In some embodiments, the additional pharmaceutical agent is JQ1 or NVP2,and the disease to be treated is leukemia, e.g., acute myelogenousleukemia, myeloblastic leukemia, promyelocytic leukemia, myelomonocyticleukemia, monocytic leukemia, monoblastic leukemia, or megakaryoblasticleukemia. In certain embodiments, a pharmaceutical composition describedherein further comprises a combination of the additional pharmaceuticalagents described herein.

The inventive compounds or compositions may synergistically augmentinhibition of CDK7 induced by the additional pharmaceutical agent(s) inthe biological sample or subject. The inventive compounds orcompositions may synergistically augment inhibition of CDK12 and/orCDK13 induced by the additional pharmaceutical agent(s) in thebiological sample or subject. Thus, the combination of the inventivecompounds or compositions and the additional pharmaceutical agent(s) maybe useful in treating proliferative diseases resistant to a treatmentusing the additional pharmaceutical agent(s) without the inventivecompounds or compositions.

In some embodiments, the activity of a protein kinase is non-selectivelyinhibited by the compounds or pharmaceutical compositions describedherein. In some embodiments, the activity of a protein kinase describedherein is selectively inhibited by the compounds or pharmaceuticalcompositions described herein, compared to the activity of a differentprotein (e.g., a different protein kinase). In certain embodiments, theactivity of CDK (e.g., CDK7, CDK12, or CDK13) is selectively inhibitedby a compound or pharmaceutical composition described herein, comparedto the activity of a different protein. In certain embodiments, theactivity of CDK7 is selectively inhibited by a compound orpharmaceutical composition described herein, compared to the activity ofa different CDK protein. In certain embodiments, the activity of CDK7 isselectively inhibited by a compound or pharmaceutical compositiondescribed herein, compared to the activity of CDK12. In certainembodiments, the activity of CDK7 is selectively inhibited by a compoundor pharmaceutical composition described herein, compared to the activityof CDK13. In certain embodiments, the activity of CDK7 is selectivelyinhibited by a compound or pharmaceutical composition described herein,compared to the activity of CDK12 and the activity of CDK13. In certainembodiments, the activity of CDK12 is selectively inhibited by acompound or pharmaceutical composition described herein, compared to theactivity of CDK7. In certain embodiments, the activity of CDK13 isselectively inhibited by a compound or pharmaceutical compositiondescribed herein, compared to the activity of CDK7. In certainembodiments, the activity of CDK12 and the activity of CDK13 areselectively inhibited by a compound or pharmaceutical compositiondescribed herein, compared to the activity of CDK7.

The selectivity of a compound or pharmaceutical composition describedherein in inhibiting the activity of a protein kinase over a differentprotein (e.g., a different protein kinase) may be measured by thequotient of the IC50 value of the compound or pharmaceutical compositionin inhibiting the activity of the different protein over the IC50 valueof the compound or pharmaceutical composition in inhibiting the activityof the protein kinase. The selectivity of a compound or pharmaceuticalcomposition described herein for a protein kinase over a differentprotein may also be measured by the quotient of the K_(d) value of anadduct of the compound or pharmaceutical composition and the differentprotein over the K_(d) value of an adduct of the compound orpharmaceutical composition and the protein kinase. In certainembodiments, the selectivity is at least 2-fold, at least 3-fold, atleast 5-fold, at least 10-fold, at least 30-fold, at least 100-fold, atleast 300-fold, at least 1,000-fold, at least 3,000-fold, at least10,000-fold, at least 30,000-fold, or at least 100,000-fold. In certainembodiments, the selectivity is not more than 100,000-fold, not morethan 10,000-fold, not more than 1,000-fold, not more than 100-fold, notmore than 10-fold, or not more than 2-fold. Combinations of theabove-referenced ranges (e.g., at least 2-fold and not more than10,000-fold) are also within the scope of the disclosure.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. The synthetic andbiological examples described in this application are offered toillustrate the compounds, pharmaceutical compositions, and methodsprovided herein and are not to be construed in any way as limiting theirscope.

Synthesis of the Compounds

The compounds provided herein can be prepared from readily availablestarting materials using the following general methods and procedures.Reactions were monitored by thin layer chromatography (TLC) with 0.25 mmE. Merck pre-coated silica gel plates (60 F₂₅₄) and Waters LCMS system(Waters 2489 UV/Visible Detector, Waters 3100 Mass, Waters 515 HPLCpump, Waters 2545 Binary Gradient Module, Waters Reagent Manager, Waters2767 Sample Manager) using SunFire™ C18 column (4.6×50 mm, 5 μm particlesize): solvent gradient=95% A at 0 min, 0% A at 5 min; solvent A=0.5%TFA in Water; solvent B=Methanol; flow rate: 1.5 mL/min. Purification ofreaction products was carried out by flash chromatography usingCombiFlash® Rf with Teledyne Isco RediSep® Rf High Performance Gold orSilicycle SiliaSep™ High Performance columns (4 g, 12 g, 24 g, 40 g, 80g or 120 g) or by Waters preparative HPLC system with a C18 column:solvent gradient=100% A at 0 min, 0% A at 15 min; solvent A=0.5% TFA inWater; solvent B=Methanol; flow rate: 20 mL/min. The purity of allcompounds was over 95% and was analyzed with Waters LCMS system. ¹H NMRand ¹³C NMR spectra were obtained using a Varian Inova-600 or 400 MHzspectrometer. Chemical shifts are reported relative to chloroform(δ=7.24) for ¹H NMR or dimethyl sulfoxide (δ=2.50) for ¹H NMR anddimethyl sulfoxide (δ=39.51) for ¹³C NMR. Data are reported as(br=broad, s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet).

Example 1.4-Acrylamido-N-(3-((2-(2-(2-hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide(THZ-4-124-1)

The synthesis of THZ-4-124-1 follows Synthetic Scheme 1. The reagentsand conditions used for the synthesis are: (1) NMP, DIPEA, 100° C. (2)pyridine, 80° C. (3) NMP, 135° C. (4) SnCl₂, Ethyl acetate and Methanol(5) acryl chloride, acetonitrile, 0° C.

N1-(2-Fluoro-9-isopropyl-9H-purin-6-yl)benzene-1,3-diamine

To a solution of 6-chloro-2-fluoro-9-isopropyl-9H-purine (214 mg) in NMP(N-Methyl-2-pyrrolidone) was added benzene-1,3-diamine (130 mg, 1.2equiv) and diisopropylethylamine (129 mg, 1.0 equiv). The solution washeated for 2 h at 100° C. The cooled solution was diluted with 100 mL ofethyl acetate and then washed with water. The separation by silica gelwith CH₂Cl₂/methanol (10/1) to give of the product (225 mg, 79%).

N-(3-((2-Fluoro-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-nitrobenzamide

To a stirred solution of the above product (225 mg, 0.80 mmol) in 10 mLof pyridine was added 4-nitrobenzoyl chloride (219 mg, 1.5 equiv) andresulting solution was heated to 80° C. The reaction mixture was stirredfor 2 h and concentrated under reduced pressure. The crude was purifiedby silica gel with CH₂Cl₂/methanol (10/1) to give of the product (285mg, 82%).

N-(3-((2-(2-(2-Hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-nitrobenzamide

The nitro compound (285 mg, 0.65 mmol) obtained from above reaction wasdissolved in 3 mL of NMP and then was added with2-(piperidin-2-yl)ethanol (170 mg, 2.0 equiv). The solution was heatedto 135° C. for 2h and then cooled down to RT. The product was purifiedby HPLC to give the product (105 mg, 30%).

4-Amino-N-(3-((2-(2-(2-hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide

The nitro compound from step 3 (105 mg, 0.19 mmol) was suspended in 5 mLof ethyl acetate/methanol (5:1) and treated with SnCl₂ (91 mg, 2.5equiv). After stirring for 2 h at 80° C., the reaction mixture wascooled to room temperature and poured into saturated aqueous NaHCO₃. Themixture was stirred for 10 min and the aqueous phase was then extractedwith 30 mL of chloroform and 2-propanol (4:1). The combined organiclayer was washed with water and brine, dried over MgSO₄, filteredthrough a pad of celite and concentrated under reduced pressure. Theresulting crude product was purified by flash column chromatography withCH₂Cl₂/methanol (10/1) to provide the title compound (68 mg, 70%).

4-Acrylamido-N-(3-((2-(2-(2-hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide

To the solution of the aniline (26 mg, 0.05 mmol)) obtained above in 5mL of acetonitrile was added diisopropylethylamine (13 mg, 2.0 equiv).The reaction mixture was cooled to 0° C. and then treated with4-chlorobut-2-enoyl chloride (15 mg, 3.0 equiv) in CH₂Cl₂. After thestirring for 10 min at 0° C., the reaction was then quenched with Sat.NaHCO₃ and extracted with 30 mL of chloroform and 2-propanol (4:1). Thesolvent was removed at reduce pressure and the crude was purified withHPLC to give the final product THZ-4-124-1 (15 mg, 55%) MS 569 (M+1), ¹HNMR (DMSO-d6): 10.42 (s, 1H), 10.15 (s, 1H), 9.53 (s, 1H), 8.40 (d,J=12.0 Hz, 2H), 7.93 (d, J=7.2 Hz, 2H), 7.79 (d, J=7.2 Hz, 2H), 7.52 (d,J=7.2 Hz, 1H), 7.27 (m, 2H), 6.43 (m, 1H), 6.28 (d, J=15 Hz, 1H), 5.78(d, J=9.6 Hz, 1H), 4.99 (s, 1H), 4.65 (m, 2H), 3.45 (m, 2H), 2.88 (t,J=6.8 Hz, 1H), 1.85 (m, 1H), 1.72 (m, 1H), 1.52 (s, 6H), 1.61-1.30 (m,12H).

Example 2.4-Acrylamido-N-(3-((2-((trans-4-(dimethylamino)cyclohexyl)amino)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide(THZ-5-38-1)

The synthesis of THZ-4-124-1 follows Synthetic Scheme 2. The reagentsand conditions used for the synthesis are: (1) pyridine, 80° C. (2) NMP,135° C. (3) SnCl₂, Ethyl acetate and Methanol (4) acryl chloride,acetonitrile, 0° C.

N-(3-((2-Fluoro-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-nitrobenzamide

To a stirred solution ofN1-(2-fluoro-9-isopropyl-9H-purin-6-yl)benzene-1,3-diamine (286 mg, 1.0mmol) in 10 mL of pyridine was added 4-nitrobenzoyl chloride (277 mg,1.5 equiv) and resulting solution was heated to 80° C. The reactionmixture was stirred for 2 h and concentrated under reduced pressure. Thecrude was purified by silica gel with CH₂Cl₂/methanol (10/1) to give ofthe product (326 mg, 75%)

N-(3-((2-(((1r,4r)-4-(dimethylamino)cyclohexyl)amino)-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-nitrobenzamide

The nitro compound (326 mg, 0.75 mmol) obtained from above reaction wasdissolved in 3 mL of NMP and then was added withtrans-N1,N1-dimethylcyclohexane-1,4-diamine (213 mg, 2.0 equiv). Thesolution was heated to 135° C. for 2h and then cooled down to RT. Theproduct was purified by HPLC to give the product (208 mg, 50%).

4-Amino-N-(3-((2-((trans-4-(dimethylamino)cyclohexyl)amino)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide

The nitro compound from step 2 (208 mg, 0.37 mmol) was suspended in 5 mLof ethyl acetate/methanol (5:1) and treated with SnCl₂ (177 mg, 2.5equiv). After stirring for 2 h at 80° C., the reaction mixture wascooled to room temperature and poured into saturated aqueous NaHCO₃. Themixture was stirred for 10 min and the aqueous phase was then extractedwith 30 mL of chloroform and 2-propanol (4:1). The combined organiclayer was washed with water and brine, dried over MgSO₄, filteredthrough a pad of celite and concentrated under reduced pressure. Theresulting crude product was purified by flash column chromatography withCH₂Cl₂/methanol (10/1) to provide the title compound (126 mg, 65%).

4-Acrylamido-N-(3-((2-((trans-4-(dimethylamino)cyclohexyl)amino)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide

To the solution of the aniline (26 mg, 0.05 mmol)) obtained above in 5mL of acetonitrile was added diisopropylethylamine (13 mg, 2.0 equiv).The reaction mixture was cooled to 0° C. and then treated with4-chlorobut-2-enoyl chloride (15 mg, 3.0 equiv) in CH₂Cl₂. After thestirring for 10 min at 0° C., the reaction was then quenched with Sat.NaHCO₃ and extracted with 30 mL of chloroform and 2-propanol (4:1). Thesolvent was removed at reduce pressure and the crude was purified withHPLC to give the final product (17 mg, 60%) MS 582 (M+1), ¹H NMR(DMSO-d6): 10.45 (s, 1H), 10.17 (s, 1H), 9.63 (br, 1H), 9.43 (br, 1H),8.26 (br, 1H), 8.25 (s, 1H), 7.98 (d, J=7.2 Hz, 2H), 7.79 (d, J=7.2 Hz,2H), 7.65 (br, 1H), 7.45 (br, 1H), 7.28 (t, J=7.8 Hz, 1H), 6.48 (m, 1H),6.28 (d, J=15 Hz, 1H), 5.78 (d, J=9.6 Hz, 1H), 4.62 (m, 1H), 2.75-2.60(m, 2H), 2.55 (s, 6H), 2.22-1.65 (m, 4H), 1.51 (d, J=6.6 Hz, 6H),1.55-1.25 (m, 4H).

Example 3.4-((E)-4-(Dimethylamino)but-2-enamido)-N-(3-((2-(((1r,4r)-4-(dimethylamino)cyclohexyl)amino)-9-isopropyl-9H-purin-6-yl)amino)phenyl)benzamide(THZ-3-49-1)

To the solution of the aniline (53 mg) obtained above in 10 mL ofacetonitrile was added diisopropylethylamine (26 mg, 2.0 equiv). Thereaction mixture was cooled to 0° C. and then treated with4-chlorobut-2-enoyl chloride (54 mg, 3.0 equiv) in CH₂Cl₂. The reactionmixture was stirred for 10 min at 0° C. and then treated with a solutionof dimethylamine in THF (3 mL, 1M). The reaction mixture was then warmedto room temperature, stirred for 1 h and concentrated under reducedpressure. The resulting crude product was purified by preparative HPLCto give the final product (28.8 mg, 45%). MS 639 (M+1).

Example 4.(E)-N-(3-((2-(3-Aminopiperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-(4-(dimethylamino)but-2-enamido)benzamide(THZ-4-119-1)

The synthesis of THZ-4-119-1 follows Synthetic Scheme 4. The reagentsand conditions used for the synthesis are: (1) NMP, 135° C. (2) SnCl₂,Ethyl acetate and Methanol (3) a) 4-bromobut-2-enoyl chloride, CH₃CN,NHMe₂, 0° C.-RT b) TFA, CHCl₃.

tert-butyl(1-(9-iso-Propyl-6-((3-(4-nitrobenzamido)phenyl)amino)-9H-purin-2-yl)piperidin-3-yl)carbamate

To a stirred solution ofN-(3-((2-fluoro-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-nitrobenzamide(435 mg) in NMP (3 mL) was added tert-butyl piperidin-3-ylcarbamate (300mg, 1.5 equiv) and then the resulting solution was heated to 130° C. for6 h. After cooling down to RT, the solution was then extracted withethyl acetate, washed with water and brine and then dried on Na₂SO₄. Thecrude was obtained after removing the solvent and then was used in thenext step directly.

tert-butyl(1-(6-((3-(4-Aminobenzamido)phenyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-3-yl)carbamate

The crude from step 1 was suspended in 5 mL of ethyl acetate/methanol(5:1) and treated with SnCl₂ (562 mg, 2.5 equiv). After stirring for 2 hat 80° C., the reaction mixture was cooled to room temperature andpoured into saturated aqueous NaHCO₃. The mixture was stirred for 10 minand the aqueous phase was then extracted with 30 mL of chloroform and2-propanol (4:1). The combined organic layer was washed with water andbrine, dried over MgSO₄, filtered through a pad of celite andconcentrated under reduced pressure. The resulting crude product waspurified by flash column chromatography with CH₂Cl₂/methanol (10/1) toprovide the product (230 mg, 40% from two steps).

(E)-N-(3-((2-(3-Aminopiperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)-4-(4-(dimethylamino)but-2-enamido)benzamide

To the solution of the aniline (58 mg) obtained above in 10 mL ofacetonitrile was added diisopropylethylamine (26 mg, 2.0 equiv). Thereaction mixture was cooled to 0° C. and then treated with4-chlorobut-2-enoyl chloride (54 mg, 3.0 equiv) in CH₂Cl₂. The reactionmixture was stirred for 10 min at 0° C. and then treated with a solutionof dimethylamine in THF (3 mL, 1M). The reaction mixture was then warmedup to room temperature, stirred for 1 h and concentrated under reducedpressure. The resulting crude product was then dissolved in CHCl₃ (3 mL)and TFA (1 mL). The solution was then allowed for stirring for 2 h.After removing the solvent, the crude was purified by preparative HPLCto give the final product (24.8 mg, 35%). MS 597 (M+1)¹H NMR (DMSO-d6):10.64 (s, 1H), 10.20 (s, 1H), 10.01 (br, 1H), 9.56 (s, 1H), 8.60 (s,1H), 8.17 (s, 1H), 8.02 (m, 3H), 7.95 (d, J=7.2 Hz, 2H), 7.80 (d, J=7.2Hz, 2H), 7.45 (d, J=8.4 Hz, 1H), 7.26 (t, J=7.8 Hz, 1H), 7.20 (d, J=8.4Hz, 1H), 6.78 (m, 1H), 6.50 (d, J=15 Hz, 1H), 4.66 (m, 1H), 4.53 (m,1H), 4.21 (m, 1H), 3.96 (d, J=7.2 Hz, 2H), 3.37-3.25 (m, 4H), 2.83 (s,6H), 1.97 (m, 1H), 1.76 (m, 1H), 1.59-1.55 (m, 2H), 1.50 (d, J=6.6 Hz,6H).

Example 5.(E)-N-(3-((5-(3-Aminopiperidin-1-yl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)amino)phenyl)-4-(4-(dimethylamino)but-2-enamido)benzamide(THZ-4-128-1)

The synthesis of THZ-4-128-1 follows Synthetic Scheme 5. The reagentsand conditions used for the synthesis are: (1) a) NMP, DIPEA, 100° C. b)TFA, CHCl₃ (2) pyridine, 80° C. (3) NMP, DIPEA, 135° C. (4) SnCl₂, Ethylacetate and Methanol (5) a) 4-bromobut-2-enoyl chloride, CH₃CN, NHMe₂,0° C.-RT b) TFA, CHCl₃.

N1-(5-Chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)benzene-1,3-diamine

To a solution of 5,7-dichloro-3-ethylpyrazolo[1,5-a]pyrimidine (215 mg)in NMP (N-Methyl-2-pyrrolidone) was added tert-butyl(3-aminophenyl)carbamate (230 mg, 1.1 equiv) and diisopropylethylamine(129 mg, 1.0 equiv). The solution was heated for 2 h at 100° C. Thecooled solution was diluted with 100 mL of ethyl acetate and then washedwith water. After removing the solvent, the crude was obtained which wasdissolved in CHCl₃ (3 mL) and TFA (1 mL). The resulting solution wasstirred for 1 h and then the solvent was removed in the reducedpressure. The crude was then purified by silica gel with CH₂Cl₂/methanol(10/1) to give the product (215 mg, 75%).

N-(3-((5-Chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)amino)phenyl)-4-nitrobenzamide

To a stirred solution of the above product (215 mg, 0.75 mmol) in 10 mLof pyridine was added 4-nitrobenzoyl chloride (210 mg, 1.5 equiv) andresulting solution was heated to 80° C. The reaction mixture was stirredfor 2 h and concentrated under reduced pressure. The crude was purifiedby silica gel with CH₂Cl₂/methanol (10/1) to give the product (212 mg,65%).

tert-Butyl(1-(3-ethyl-7-((3-(4-nitrobenzamido)phenyl)amino)pyrazolo[1,5-a]pyrimidin-5-yl)piperidin-3-yl)carbamate

To a stirred solution of the product from step 2 (212 mg) in NMP (3 mL)was added tert-butyl piperidin-3-ylcarbamate (145 mg, 1.5 equiv) andthen the resulting solution was heated to 130° C. for 6 h. After coolingdown to RT, the solution was then extracted with ethyl acetate washedwith water and brine and dried on Na₂SO₄. The crude was obtained afterremoving the solvent and then was used in the next step directly.

tert-butyl(1-(7-((3-(4-Aminobenzamido)phenyl)amino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-3-yl)carbamate

The crude from step 3 was suspended in 5 mL of ethyl acetate/methanol(5:1) and treated with SnCl₂ (281 mg, 2.5 equiv). After stirring for 2 hat 80° C., the reaction mixture was cooled to room temperature andpoured into saturated aqueous NaHCO₃. The mixture was stirred for 10 minand the aqueous phase was then extracted with 30 mL of chloroform and2-propanol (4:1). The combined organic layer was washed with water andbrine, dried over MgSO₄, filtered through a pad of celite andconcentrated under reduced pressure. The resulting crude product waspurified by flash column chromatography with CH₂Cl₂/methanol (10/1) toprovide the product (82 mg, 30% from two steps).

(E)-N-(3-((5-(3-Aminopiperidin-1-yl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)amino)phenyl)-4-(4-(dimethylamino)but-2-enamido)benzamide

To the solution of the aniline (57 mg) obtained above in 10 mL ofacetonitrile was added diisopropylethylamine (26 mg, 2.0 equiv). Thereaction mixture was cooled to 0° C. and then treated with4-chlorobut-2-enoyl chloride (54 mg, 3.0 equiv) in CH₂Cl₂. The reactionmixture was stirred for 10 min at 0° C. and then treated with a solutionof dimethylamine in THF (3 mL, 1M). The reaction mixture was then warmedto room temperature, stirred for 1 h and concentrated under reducedpressure. The resulting crude product was then dissolved in CHCl₃ (3 mL)and TFA (1 mL). The solution was then allowed for stirring for 2 h.After removing the solvent, the crude was purified by preparative HPLCto give the final product (15 mg, 25%). MS 582 (M+1)¹H NMR (DMSO-d6):10.64 (s, 1H), 10.32 (s, 1H), 10.09 (br, 1H), 9.44 (s, 1H), 8.03 (m,1H), 7.98 (br, 2H), 7.95 (d, J=7.2 Hz, 2H), 7.80 (d, J=7.2 Hz, 2H), 7.43(d, J=8.4 Hz, 1H), 7.37 (t, J=7.8 Hz, 1H), 7.15 (d, J=8.4 Hz, 1H), 6.78(m, 1H), 6.50 (d, J=15 Hz, 1H), 6.06 (s, 1H), 4.31 (m, 1H), 3.96 (d,J=7.2 Hz, 2H), 3.86 (m, 1H), 3.20-3.10 (m, 3H), 2.79 (s, 6H), 2.59 (q,J=8.4 Hz, 2H), 1.97 (m, 1H), 1.76 (m, 1H), 1.59 (m, 2H), 1.23 (d, J=7.8Hz, 3H).

Example 6.4-Acrylamido-N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-24)

4-Acrylamido-N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-24)

The mixture of SB1-E-23-1 (100 mg, 0.263 mmol), SB1-E-22-1 (100 mg,0.523 mmol), HATU (200 mg, 0.526 mmol), DIPEA (0.5 mL) and DMF (5 mL)was stirred at r.t overnight. After completion, the mixture was purifiedby prep-TLC (DCM/MeOH=15/1) and prep-HPLC (C18 column, CH₃CN/H₂O,containing 0.05% NH₄HCO₃) to obtain SB1-E-24 (off-white solid, 23 mg,16%). HPLC: 99% (254 nm); LCMS (m/z): 554 [M+H]⁺; ¹H NMR (DMSO-d₆, 500MHz): δ 10.45 (s, 1H), 10.27 (s, 1H), 9.63 (bs, 1H), 8.01 (s, 1H), 7.97(d, J=9.0 Hz, 2H), 7.83 (m, 3H), 7.49 (d, J=8.5 Hz, 1H), 7.39 (t, J=8.5Hz, 1H), 7.19 (d, J=7.5 Hz, 1H), 6.48 (dd, J₁=16.5 Hz, J₂=10.5 Hz, 1H),6.31 (d, J=16.5 Hz, 1H), 6.03 (s, 1H), 5.81 (d, J=10.5 Hz, 1H), 4.58 (s,1H), 4.17 (m, 1H), 3.33-3.43 (m, 2H), 2.99 (m, 1H), 2.55-2.60 (m, 2H),1.18-1.89 (m, 12H).

Example 7.4-Acrylamido-N-(3-(5-((1r,4r)-4-(dimethylamino)cyclohexylamino)-3-isopropylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-25)

2-Formyl-3-methylbutanenitrile (SB1-E-25-1)

To a solution of SM-25-1 (10.0 g, 120 mmol) in THF (10 mL), LDA (2 M, 60ml, 120 mmol) was added slowly at −78° C. After completion, the mixturewas added to a solution of ethyl formate (9.0 g, 121.5 mmol) in THF (40ml) at −78° C. After completion, the mixture was stirred at 0° C. for3h. The solvent was removed, then water (100 mL) was added, and theresulting mixture was extracted with Et₂O (200 mL×3). The combinedorganic layer was washed with brine (100 mL×2), dried over sodiumsulfate, filtered through Celite, and concentrated under reducedpressure to give the crude SB1-E-25-1 (colorless oil, 12.5 g, 94%yield). The crude product was used directly for the next step withoutfurther purification.

4-iso-Propyl-1H-pyrazol-5-amine (SB1-E-25-2)

To a solution of SB1-E-25-1 (12.5 g, 112 mmol) in EtOH (200 mL),hydrazine hydrate (28 g, 560 mmol) and AcOH (26.9 g, 448 mmol) wasadded. The mixture was stirred at 80° C. for 4h. The solvent wasremoved, then water (200 ml) was added, and the resulting mixture wasextracted with DCM (300 mL×3). The combined organic layer was washedwith brine (100 mL×2), dried over sodium sulfate, filtered throughCelite, and concentrated under reduced pressure. The residue waspurified by column chromatography on silica gel (DCM/MeOH=15/1 to 8/1)to afford SB1-E-25-2 (yellow solid, 13.3 g, 95% yield). LCMS (m/z): 126[M+H]⁺.

3-iso-Propylpyrazolo[1,5-a]pyrimidine-5,7(4H,6H)-dione (SB1-E-25-3)

To a solution of SB1-E-25-2 (1.7 g, 13.6 mmol) in CH₃OH (20 ml), SM-25-2(5.4 g, 40.8 mmol) and sodium methoxide (3.7 g, 68 mmol) was added. Themixture was stirred at 70° C. for 4h. After completion, the solvent wasremoved, water (200 ml) was added, then 1M HCl aq. (40 mL) was added toadjust the pH to 3. The mixture was filtered and the filter residue wasevaporated to dryness under reduced pressure to give the crudeSB1-E-25-3 (off-white solid, 2.5 g, 95% yield). LCMS (m/z): 194 [M+H]⁺.

5,7-Dichloro-3-isopropylpyrazolo[1,5-a]pyrimidine (SB1-E-25-4)

To a solution of SB1-E-25-3 (2.4 g, 12.4 mmol) in CH₃CN (30 ml), POCl₃(9.4 g, 62 mmol) and N,N-dimethylaniline (4.5 g, 37.2 mmol) was added.The mixture was stirred at 80° C. for 8h. The mixture was concentratedand water (40 mL) was added. The mixture was filtered and concentratedto remove the solvent. The residue was washed with water (100 ml) andthen evaporated to dryness under reduced pressure to give the crudeSB1-E-25-4 (brown solid, 2.7 g, 85% yield). LCMS (m/z): 230 [M+H]⁺.

N¹-(5-Chloro-3-isopropylpyrazolo[1,5-a]pyrimidin-7-yl)benzene-1,3-diamine(SB1-E-25-5)

To a solution of SB1-E-25-4 (2.6 g, 11.3 mmol), in i-PrOH (20 mL),1.3-diaminobenzene (1.47 g, 13.6 mmol) and DIPEA (2.92 g, 22.6 mmol) wasadded. The mixture was stirred at 110° C. for 8h. The mixture wasconcentrated, water (20 mL) was added, and the resulting mixture wasextracted with DCM (30 mL×3). The combined organic layer was washed withbrine (20 mL×2), dried over sodium sulfate, filtered through Celite, andconcentrated under reduced pressure. The residue was purified by columnchromatography on silica gel (PE/ethyl acetate=8/1 to 4/1) to affordSB1-E-25-5 (off-white solid, 2.2 g, 65% yield). LCMS (m/z): 302 [M+H]⁺.

N7-(3-Aminophenyl)-N5-((1s,4s)-4-(dimethylamino)cyclohexyl)-3-isopropylpyrazolo[1,5-a]pyrimidine-5,7-diamine(SB1-E-25-6)

The mixture of SB1-E-25-5 (350 mg, 1.16 mmol), SB1-E-21-3 (200 mg, 1.41mmol), KF (400 mg, 6.88 mmol) and NMP (2 mL) was stirred at 170° C. for8 h, after completion, concentrated to remove the solvent, the residuewas purified by prep-TLC (DCM/MeOH=10/1) to obtain SB1-E-25-6 (lightbrown solid, 130 mg, yield 28%). LCMS (m/z): 408 [M+H]⁺.

4-Acrylamido-N-(3-(5-((1r,4r)-4-(dimethylamino)cyclohexylamino)-3-isopropylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-25)

The mixture of SB1-E-25-5 (40 mg, 0.0981 mmol), SB1-E-24-1 (35 mg, 0.183mmol), HATU (75 mg, 0.197 mmol) and DMF (5 mL) was stirred at r.tovernight. After completion, the mixture was purified by prep-TLC(DCM/MeOH=8/1) and prep-HPLC (C18 column, CH₃CN/H₂O, containing 0.05%NH₄HCO₃) to obtain SB1-E-25 (gray solid, 15 mg, yield 26%). HPLC: 97%(254 nm); LCMS (m/z): 581 [M+H]+; ¹H NMR (DMSO-d₆, 500 MHz): δ 10.44 (s,1H), 10.26 (s, 1H), 9.07 (s, 1H), 7.97 (d, J=8.5 Hz, 2H), 7.85 (s, 1H),7.82 (d, J=8.5 Hz, 2H), 7.67 (s, 1H), 7.64 (t, J=4.0 Hz, 1H), 7.37 (t,J=8.0 Hz, 1H), 7.10 (d, J=7.5 Hz, 1H), 6.62 (d, J=7.0 Hz, 1H), 6.47 (dd,J₁=17.0 Hz, J₂=10.5 Hz, 1H), 6.31 (d, J=17.0 Hz, 1H), 5.81 (d, J=10.5Hz, 1H), 3.63 (s, 1H), 3.00 (m, 1H), 1.77-2.17 (m, 11H), 1.09-1.29 (m,10H).

Example 8.4-Acrylamido-N-(3-(5-((1r,4r)-4-(dimethylamino)cyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-22)

4-Acrylamidobenzoic Acid (SB1-E-22-1)

To the solution of SM-22-1 (500 mg, 3.65 mmol) in pyridine (20 mL) wasadded acrylyl chloride (500 mg, 5.52 mmol), the mixture was stirred atr.t overnight, after completion, the mixture was poured to a ice-water(20 mL), filtered, the solid was washed with H₂O, dried to obtainSB1-E-22-1 (light yellow solid, 600 mg, yield 86%). LCMS (m/z): 192[M+H]⁺.

4-Acrylamido-N-(3-(5-((1r,4r)-4-(dimethylamino)cyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)benzamide(SB1-E-22)

The mixture of SB1-E-21-7 (50 mg, 0.127 mmol), SB1-E-22-1 (45 mg, 0.235mmol), HATU (88 mg, 0.231 mmol), DIPEA (0.3 mL) and DMF (2 mL) wasstirred at r.t overnight, after completion, concentrated to remove thesolvent, the residue was purified by prep-TLC (DCM/MeOH=10/) andprep-HPLC (C18 column, CH₃CN/H₂O, containing 0.05% NH₄HCO₃) to obtainSB1-E-22 (light gray solid, 7 mg, yield 10%). HPLC: 95% (214 nm); LCMS(m/z): 567 [M+H]⁺; ¹H NMR (DMSO-d₆, 500 MHz): δ 10.44 (s, 1H), 10.25 (s,1H), 9.06 (s, 1H), 7.97 (d, J=9.0 Hz, 2H), 7.85 (d, J=5.0 Hz, 1H), 7.82(d, J=9.0 Hz, 2H), 7.70 (s, 1H), 7.63 (d, J=8.0 Hz, 1H), 7.37 (t, J=8.5Hz, 1H), 7.10 (d, J=7.0 Hz, 1H), 6.61 (d, J=7.5 Hz, 1H), 6.47 (dd,J₁=16.5 Hz, J₂=9.5 Hz, 1H), 6.31 (d, J=16.5 Hz, 1H), 5.81 (d, J=9.5 Hz,1H), 5.63 (s, 1H), 3.68 (s, 1H), 2.54 (q, J=7.5 Hz, 2H), 2.15 (s, 6H),1.77-2.15 (m, 5H), 1.11-1.27 (m, 7H).

Example 9.4-Acrylamido-N-(3-(8-ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)benzamide(SB1-E-19)

4-Acrylamido-N-(3-(8-ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)benzamide(SB1-E-19)

A mixture of SB1-E-18-08 (70 mg, 0.18 mmol), 4-acrylamidobenzoic acid(52 mg, 0.27 mmol), HATU (68 mg, 0.18 mmol) and triethylamine (54 mg,0.54 mmol) in DCM (3 mL) was stirred at r.t overnight, diluted withdichloromethane (10 ml), washed with water (10 mL) and saturated sodiumbicarbonate solution (10 mL×2), dried over anhydrous sodium sulfatefiltered and concentrated in vacuo, purified by prep-HPLC (C18 column,CH₃CN/H₂O, containing 0.05% TFA) to get SB1-E-19, also referred toherein as E19 and E-19 (white solid, 25 mg, yield: 25%). HPLC: 100% (254nm); LCMS (m/z): 555 [M+H]⁺; ¹H NMR (DMSO-d₆, 500 MHz): δ: 10.45 (s,1H), 10.19 (s, 1H), 8.49 (s, 1H), 7.97 (d, J=8.5 Hz, 2H), 7.88 (s, 1H),7.82 (d, J=8.5 Hz, 1H), 7.45-7.51 (m, 2H), 7.34 (t, J=8.0 Hz, 1H), 6.48(dd, J=16.5, 10 Hz, 1H), 6.32 (d, J=17.0 Hz, 1H), 5.82 (d, J=10.0 Hz,1H), 5.00 (s, 1H), 4.66 (d, J=10.0 Hz, 1H), 2.91 (t, J=13.0 Hz, 1H),2.50-2.54 (m, 2H), 1.56-1.71 (m, 8H), 1.38-1.40 (m, 1H), 1.20-1.23 (m,4H).

Example 10.N-(3-(2-((1s,4s)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)phenyl)acrylamide(SB1-E-14)

tert-Butyl (1s,4s)-4-(dimethylamino)cyclohexylcarbamate (SB1-E-14-2)

To the solution of SB1-E-14-1 (1.0 g, 4.67 mmol), MeOH (30 mL) and HCHO(600 mg, 20.0 mmol) was added NaBH₃CN (1.5 g, 23.9 mmol), the mixturewas stirred at r.t overnight. After completion, concentrated to removethe solvent, then extracted with ethyl acetate (100 mL×4), the organicphase was washed with H₂O (50 mL), brine (50 mL×2), dried with Na₂SO₄.Filtered, concentrated to remove the solvent, the residue was purifiedby silica gel (DCM/MeOH=10/1, 4/1) to obtain SB1-E-14-2 (light brownsolid, 800 mg, yield 71%). LCMS (m/z): 243 [M+H]⁺.

(1s,4s)—N1,N1-Dimethylcyclohexane-1,4-diamine (SB1-E-14-3)

The mixture of SB1-E-14-2 (350 mg, 1.44 mmol), DCM (3 mL) and TFA (3 mL)was stirred at r.t for 3 h. after completion, concentrated to remove thesolvent to obtain SB1-E-14-3 (light yellow sticky oil, 200 mg, yield98%). LCMS (m/z): 143 [M+H]⁺.

2,6-Dichloro-9-isopropyl-9H-purine (SB1-E-14-4)

To a solution of SM-14-2 (3.0 g, 15.3 mmol) and 2-propanol (2.75 g, 45.9mmol) in THF (30 mL), PPh₃ (8.02 g, 30.6 mmol) was added. The mixturewas stirred at room temperature for 10 min. Then DIEA (6.18 g, 30.6mmol) was added. The final mixture was stirred at 70° C. for 3h. aftercompletion, concentrated to remove the solvent, water (30 mL) was added,the resulting mixture was extracted with DCM (50 mL×3). The combinedorganic layer was washed with brine (50 mL×2), dried over sodiumsulfate, filtered through Celite, and concentrated under reducedpressure. The residue was purified by column chromatography on silicagel (ethyl acetate/acetone=20/1 to 10/1) to afford SB1-E-14-4 (off-whitesolid, 2.34 g, 66% yield).

N1-(2-Chloro-9-isopropyl-9H-purin-6-yl)benzene-1,3-diamine (SB1-E-14-5)

The mixture of SB1-E-14-4 (1.2 g, 5.19 mmol), SM-14-3 (850 mg, 7.86mmol), n-BuOH (30 mL) and DIPEA (2 mL) was stirred at 115° C. for 4 h.after completion, concentrated to remove the solvent, the residue waspurified by silica gel (DCM/MeOH=50/1) to obtain SB1-E-14-5 (light brownsolid, 1.2 g, yield 76%). LCMS (m/z): 303 [M+H]⁺.

N6-(3-Aminophenyl)-N2-((1s,4s)-4-(dimethylamino)cyclohexyl)-9-isopropyl-9H-purine-2,6-diamine(SB1-E-14-6)

The mixture of SB1-E-14-5 (370 mg, 1.22 mmol), SB1-E-14-3 (200 mg, 1.41mmol), KF (360 mg, 6.20 mmol) and NMP (2 mL) was stirred at 172° C. for8 h. after completion, the mixture was purified by silica gel(DCM/MeOH=10/1, 8/1, 6/1) to obtain SB1-E-14-6 (brown solid, 150 mg,yield 30%). LCMS (m/z): 409 [M+H]⁺.

N-(3-(2-((1s,4s)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)phenyl)acrylamide(SB1-E-14)

To a solution of SB1-E-14-6 (60 mg, 0.147 mmol), DIPEA (0.5 mL) in CH₃CN(4 mL) was added the solution of acryloyl chloride (20 mg, 0.221 mmol)in CH₃CN (1 mL) dropwise, the mixture was stirred at OC for 2 h. aftercompletion, concentrated to remove the solvent, the residue was purifiedby prep-TLC (DCM/MeOH=30/1) and prep-HPLC (C18 column, CH₃CN/H₂O,containing 0.05% NH₄HCO₃) to obtain SB1-E-14 (off-white solid, 20 mg,yield 29%). HPLC: 100% (254 nm); LCMS (m/z): 463 [M+H]+; ¹H NMR(DMSO-d₆, 400 MHz): δ 10.04 (s, 1H), 9.38 (s, 1H), 8.44 (s, 1H), 7.95(s, 1H), 7.63 (d, J=7.2 Hz, 1H), 7.25 (s, 1H), 7.20 (t, J=8.0 Hz, 1H),6.47 (dd, J₁=16.8 Hz, J₂=9.6 Hz, 1H), 6.26 (d, J=16.8 Hz, 1H), 5.75 (d,J=9.6 Hz, 1H), 4.59 (m, 1H), 3.95 (m, 1H), 2.20 (s, 6H), 2.07 (m, 1H),1.48-1.76 (m, 14H).

Example 11.N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)cyclohexyl)acrylamide(SB1-E-15)

tert-butyl3-(2-Chloro-9-isopropyl-9H-purin-6-ylamino)cyclohexylcarbamate(SB1-E-15-2)

The mixture of SB1-E-15-1 (520 mg, 2.25 mmol), SM-15-2 (490 mg, 2.29mmol), n-BuOH (15 mL) and DIPEA (1 mL) was stirred at 100° C. overnight,after completion, concentrated to remove the solvent, the residue waspurified by silica gel (PE/ethyl acetate=2/1) to obtain SB1-E-15-2(light brown solid, 380 mg, yield 41%). LCMS (m/z): 409 [M+H]⁺.

tert-butyl3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)cyclohexylcarbamate(SB1-E-15-3)

The mixture of SB1-E-15-2 (180 mg, 0.440 mmol), 4 (150 mg, 1.05 mmol),KF (110 mg, 1.89 mmol) and n-BuOH (1.5 mL) was stirred at 135° C.overnight, after completion, concentrated to remove the solvent, theresidue was purified by prep-TLC (DCM/MeOH=6/1) to obtain SB1-E-15-3(light brown solid, 25 mg, yield 11%). LCMS (m/z): 515 [M+H]⁺.

N6-(3-Aminocyclohexyl)-N2-((1r,4r)-4-(dimethylamino)cyclohexyl)-9-isopropyl-9H-purine-2,6-diamine(SB1-E-15-4)

The mixture of SB1-E-15-3 (25 mg, 0.0486 mmol), DCM (3 mL) and TFA (3mL) was stirred at r.t overnight. after completion, concentrated toremove the solvent to obtain SB1-E-15-4 (light brown sticky oil, 20 mg,yield 95%). LCMS (m/z): 415 [M+H]⁺.

N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)cyclohexyl)acrylamide(SB1-E-15)

To a solution of SB1-E-15-4 (20 mg, 0.0482 mmol), CH₃CN (4 mL) and DIPEA(0.5 mL) was added acryloyl chloride (7 mg, 0.0773 mmol) in CH₃CN (1 mL)dropwise, the mixture was stirred at r.t overnight. After completion,the mixture was purified by prep-TLC (DCM/MeOH=8/1) and prep-HPLC (C18column, CH₃CN/H₂O, containing 0.05% NH₄HCO₃) to obtain SB1-E-15 (whitesolid, 5 mg, yield 24%). HPLC: 100% (254 nm); LCMS (m/z): 469 [M+H]+; ¹HNMR (DMSO-d₆, 500 MHz): δ 8.03 (m, 1H), 7.79 (s, 1H), 6.79 (s, 1H), 6.34(dd, J₁=17.0 Hz, J₂=12.0 Hz, 1H), 6.07 (d, J=17.0 Hz, 1H), 5.56 (d,J=12.0 Hz, 1H), 4.51 (m, 1H), 4.07 (s, 1H), 3.61 (s, 1H), 2.22 (s, 7H),2.00 (s, 2H), 1.81 (m, 5H), 1.19-1.65 (m, 17H).

Example 12.N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)benzyl)acrylamide(SB1-E-16)

tert-butyl 3-(2-Chloro-9-isopropyl-9H-purin-6-ylamino)benzylcarbamate(SB1-E-16-3)

The mixture of SB1-E-16-2 (500 mg, 2.16 mmol), SB1-E-16-1 (490 mg, 2.20mmol), n-BuOH (20 mL) and DIPEA (1 mL) was stirred at 90° C. overnight,after completion, concentrated to remove the solvent, the residue waspurified by silica gel (PE/ethyl acetate=2/1) to obtain SB1-E-16-3(off-white solid, 360 mg, yield 40%). LCMS (m/z): 417 [M+H]⁺.

tert-butyl3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)benzylcarbamate(SB1-E-16-4)

The mixture of SB1-E-16-3 (210 mg, 0.504 mmol), 4 (150 mg, 1.05 mmol),KF (90 mg, 1.55 mmol) and n-BuOH (2 mL) was stirred at 135° C. for 2days, after completion, concentrated to remove the solvent, the residuewas purified by prep-TLC (DCM/MeOH=10/1) to get SB1-E-16-4 (light yellowsolid, 90 mg, yield 34%. LCMS (m/z): 523 [M+H]⁺.

N6-(3-(Aminomethyl)phenyl)-N2-((1r,4r)-4-(dimethylamino)cyclohexyl)-9-isopropyl-9H-purine-2,6-diamine(SB1-E-16-5)

The mixture of SB1-E-16-4 (50 mg, 0.0957 mmol), DCM (5 mL) and TFA (3mL) was stirred at r.t overnight, after completion, concentrated toremove the solvent to get SB1-E-16-5 (light brown solid, 40 mg, 95%).LCMS (m/z): 423 [M+H]⁺.

N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-9-isopropyl-9H-purin-6-ylamino)benzyl)acrylamide(SB1-E-16)

To a solution of SB1-E-16-5 (40 mg, 0.0947 mmol), CH₃CN (9 mL) and DIPEA(1 mL) was added acryloyl chloride (13 mg, 0.144 mmol) in CH₃CN (1 mL)dropwise, the mixture was stirred at r.t overnight, after completion,concentrated to remove the solvent, the residue was purified by prep-TLC(DCM/MeOH=8/1) and prep-HPLC (C18 column, CH₃CN/H₂O, containing 0.05%NH₄HCO₃) to obtain SB1-E-16 (white solid, 4.5 mg, yield 10%). HPLC: 95%(214 nm); LCMS (m/z): 477 [M+H]+; ¹H NMR (DMSO-d₆, 500 MHz): δ 9.40 (s,1H), 8.60 (d, 1H), 7.94 (s, 1H), 7.88 (d, 1H), 7.22 (t, J=8.0 Hz, 1H),6.87 (d, J=7.5 Hz, 1H), 6.30 (dd, J₁=17.0 Hz, J₂=10.0 Hz, 1H), 6.14 (d,J=17.0 Hz, 1H), 5.62 (d, J=10.0 Hz, 1H), 4.57 (m, 1H), 4.36 (d, J=6.0Hz, 2H), 1.84-2.36 (m, 10H), 1.49 (s, 3H), 1.46 (s, 3H), 1.23-1.34 (m,5H).

Example 13.N-(3-((2-(2-(2-Hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)acrylamide(THZ-4-134-1)

2-(1-(6((3-Aminophenyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol

The mixture of SB1-E-14-5 (1.1 g, 3.72 mmol), SM-23-1 (800 mg, 6.19mmol), KF (1.0 g, 17.2 mmol) and NMP (3 mL) was stirred at 168° C. for12 h, after completion, concentrated to remove the solvent, the residuewas purified by silica gel (PE/ethyl acetate=2/1, 1/1) to obtain desiredproduct (1.2 g, yield 81%). LCMS (m/z): 396 [M+H]⁺.

N-(3-((2-(2-(2-Hydroxyethyl)piperidin-1-yl)-9-isopropyl-9H-purin-6-yl)amino)phenyl)acrylamide(THZ-4-134-1)

To a solution of free amine obtained from above reaction (30 mg, 0.076mmol), DIPEA (0.7 mL) in CH₃CN (12 mL) was added the solution ofacryloyl chloride (11 mg, 0.12 mmol) in CH₃CN (2 mL) dropwise, themixture was stirred at 0° C. for 3 h. after completion, concentrated toremove the solvent, the residue was purified by prep-TLC (DCM/MeOH=30/1)and prep-HPLC (C18 column, CH₃CN/H₂O, containing 0.05% NH₄HCO₃) toobtain THZ-4-134-1 (off-white solid, 23 mg, yield 70%). HPLC: 98% (254nm); LCMS (m/z): 450 [M+H]⁺; ¹H NMR (DMSO-d₆, 600 MHz): δ 10.42 (s, 1H),9.50 (s, 1H), 8.34 (s, 1H), 7.25 (s, 1H), 7.52 (d, J=7.8 Hz, 1H),7.25-7.16 (m, 2H), 6.45 (dd, J₁=17.2 Hz, J₂=10.0 Hz, 1H), 6.27 (d,J=17.2 Hz, 1H), 5.77 (d, J=10.0 Hz, 1H), 4.97 (br, 1H), 4.61 (m, 1H),3.34-3.38 (m, 3H), 2.87 (t, J=12 Hz, 1H), 1.83 (m, 1H), 1.74 (m, 1H),1,69 (m, 3H), 1.60-1.50 (m, 9H), 1.34 (m, 1H).

Example 14.N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(compound SB1-E-17)

N4-(3-Aminophenyl)-N2-((1r,4r)-4-(dimethylamino)cyclohexyl)-8-ethylpyrazolo[1,5-a][1,3,5]triazine-2,4-diamine(SB1-E-17-01)

To a stirred mixture of SB1-E-18-07 (60 mg, 0.14 mmol) and SB1-E-21-3(30 mg, 0.21 mmol) in N-methyl-2-pyrrolidone (1 mL) was added KF (24 mg,0.42 mmol). This mixture was heated at 170° C. for 3 h, cooled to r.t,filtered, purified by prep-TLC (DCM/MeOH=6/1) to get SB1-E-17-01 (whitesolid, 40 mg, yield: 73%). MS (ESI): m/z 395 [M+H]⁺.

N-(3-(2-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(compound SB1-E-17)

To a solution of SB1-E-17-01 (40 mg, 0.10 mmol) in THF (1 mL) was addedAcryloyl chloride (14 mg, 0.15 mmol) and Triethylamine (30 mg, 0.30mmol) was stirred at r.t for 2 h. After completion, the reaction mixturewas diluted with dichloromethane (10 ml), washed with water (10 mL) andsaturated sodium bicarbonate solution (10 mL×2), dried over anhydroussodium sulfate, concentrated, purified by prep-HPLC (C18 column,CH₃CN/H₂O, containing 0.05% NH₄HCO₃) to get SB1-E-17, also referred toherein as E17 and E-17 (white solid, 4 mg, yield: 11%). MS (ESI): m/z449 [M+H]⁺. ¹H NMR (300 MHz, DMSO) δ: 9.98 (s, 1H), 9.65 (s, 1H), 8.14(s, 1H), 7.76 (s, 1H), 7.52 (d, J=8.1 Hz, 1H), 7.45 (d, J=7.8 Hz, 1H),7.29 (t, J=8.1 Hz, 1H), 6.64 (s, 1H), 6.42-6.51 (m, 1H), 6.23-6.29 (m,1H), 5.70-5.74 (m, 1H), 3.69-3.72 (m, 1H), 2.51-2.56 (m, 2H), 2.36 (s,6H), 2.03-2.06 (m, 2H), 1.86-1.90 (m, 2H), 1.18-1.37 (m, 8H).

Example 15.N-(3-(8-Ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(SB1-E-18)

ethyl N-[(4-Ethyl-1H-pyrazol-5-yl)carbamothioyl]carbamate (SB1-E-18-01)

To a solution of SM-18-1 (2.8 g, 25.2 mmol) in ethanol (50.0 mL) wasadded ethoxycarbonyl isothiocyanate (3.3 g, 25.2 mL) in one portion atr.t. The mixture was stirred at 80° C. overnight. The reaction mixturewas concentrated under reduced pressure to afford the residue, purifiedby flash column chromatography (PE/ethyl acetate=3/1) to get SB1-E-18-01(white solid, 4 g, yield: 65%). LCMS (m/z): 243 [M+H]⁺.

8-Ethyl-2-thioxo-2,3-dihydropyrazolo[1,5-a][1,3,5]triazin-4((1H)-one(SB1-E-18-02)

To a solution of SB1-E-18-01 (3.9 g, 16.1 mmol) in acetonitrile (40 mL)was added K₂CO₃ (6.67 g, 48.3 mmol) in one portion at r.t. The mixturewas heated at 85° C. overnight, cooled, acidified with AcOH. The solidwas filtered off to get SB1-E-18-02 (yellow solid, 2.1 g, yield: 66%).LCMS (m/z): 197 [M+H]⁺.

8-Ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4(3H)-one(SB1-E-18-03)

To a stirred mixture of SB1-E-18-02 (2.1 g, 10.7 mmol) and NaOH (0.86 g,21.4 mmol) in Dioxane/H₂O (30/8 mL) was added iodomethane (1.52 g, 10.7mol). This mixture was stirred at r.t for 1 h, acidified withHydrochloric acid, concentrated to remove the solvent, the residue waspurified by silica gel (DCM/MeOH=30/1) to get SB1-E-18-03 (white solid,2.0 g, yield: 89%). LCMS (m/z): 211 [M+H]⁺.

4-Chloro-8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazine(SB1-E-18-04)

To a stirred mixture SB1-E-18-03 (2.0 g, 9.5 mmol) and N,N-dimethylaniline (2.3 g, 19.0 mmol) in acetonitrile (10 mL) under argon was addedPOCl₃ (20 ml, 219 mol). This mixture was heated at 85° C. overnight,cooled, the reaction mixture was concentrated under reduced pressure toafford the residue SB1-E-18-04 (white solid, 2.2 g, yield: 100% usednext step directly). LCMS (m/z): 229 [M+H]⁺.

N1-(8-Ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-yl)benzene-1,3-diamine(SB1-E-18-05)

To a stirred mixture SB1-E-18-04 (2.2 g, 9.5 mmol), benzene-1,3-diamine(1.23 g, 11.4 mmol) and NaHCO₃ (130.4 mg, 0.95 mmol) in acetonitrile (25mL). This mixture was heated at 75° C. overnight, cooled, filtered andconcentrated to remove the solvent, the residue was purified by silicagel (PE/ethyl acetate=3/1 to 1/1) to get SB1-E-18-05 (white solid, 1.1g, yield: 38%). LCMS (m/z): 301 [M+H]⁺.

tert-Butyl3-(8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenylcarbamate (SB1-E-18-06)

To a solution of SB1-E-18-05 (1.1 g, 3.67 mmol) in MeOH (20.0 mL) wasadded Di-tert-butyl dicarbonate (1.2 g, 5.5 mmol) and TEA (1.1 g, 11.0mmol) in one portion at r.t. The reaction was stirred at r.t. overnight.The reaction mixture was concentrated under reduced pressure to affordthe residue, purified by flash column chromatography (PE/ethylacetate=3/1) to get SB1-E-18-06 (white solid, 1.26 g, yield: 86%). LCMS(m/z): 401 [M+H]⁺.

tert-Butyl3-(8-ethyl-2-(methylsulfonyl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenylcarbamate (SB1-E-18-07)

To a solution of SB1-E-18-06 (600 mg, 1.5 mmol) in DCM (15 mL) was added3-Chloroperbenzoic acid (776 mg, 4.5 mmol) in one portion at r.t. Themixture was stirred at r.t for 1 h. The reaction mixture was quenchedwith sat Na₂S₂O₃ solution (10 mL), diluted with DCM (50 mL)and washedwith saturated aqueous NaCl (3×50 mL), dried over anhydrous Na₂SO₄,filtered and concentrated to give SB1-E-18-07 (yellow solid, 620 mg,yield: 96%), used for next step directly. LCMS (m/z): 433 [M+H]⁺.

2-(1-(4-(3-Aminophenylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-2-yl)piperidin-2-yl)ethanol (SB1-E-18-08)

To a stirred mixture SB1-E-18-07 (360 mg, 0.84 mmol) and2-(piperidin-2-yl)ethanol (215 mg, 1.67 mmol) in N-methyl-2-pyrrolidone(3 mL) was added KF (146 mg, 2.51 mmol). This mixture was heated at 170°C. for 3 h, cooled, filtered, the crude was purified by silica gel(PE/ethyl acetate=2/1) to get SB1-E-18-08 (yellow solid, 150 mg, yield:47%). LCMS (m/z): 382 [M+H]⁺.

N-(3-(8-Ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(SB1-E-18)

To a solution of SB1-E-18-08 (70 mg, 0.18 mmol) in THF (2 mL) was addedAcryloyl chloride (18 mg, 0.20 mmol) and triethylamine (54 mg, 0.54mmol) was stirred at r.t for 2 h. After completion, the reaction mixturewas diluted with dichloromethane (10 ml), washed with water (10 mL) andsaturated sodium bicarbonate solution (10 mL×2), dried over anhydroussodium sulfate, concentrated, purified by prep-HPLC (C18 column,CH₃CN/H₂O, containing 0.05% NH₄HCO₃) to get SB1-E-18, also referred toherein as E-18 and E18 (white solid, 13 mg, yield: 16%). HPLC: 100% (254nm); LCMS (m/z): 555 [M+H]⁺; ¹H NMR (DMSO-d₆, 500 MHz): δ: 10.17 (s,1H), 10.07 (s, 1H), 8.34 (s, 1H), 7.84 (s, 1H), 7.51 (s, 1H), 7.30-7.34(m, 2H), 6.46 (dd, J=17, 10.0 Hz, 1H), 6.28 (d, J=17 Hz, 1H), 5.77 (d,J=11.5 Hz, 1H), 4.98 (s, 1H), 4.65 (d, J=13 Hz, 1H), 4.56 (s, 1H), 2.88(t, J=12.5 Hz, 1H), 2.47-2.50 (m, 2H), 1.56-1.88 (m, 8H), 1.36-1.38 (m,1H), 1.19-1.23 (m, 4H).

Example 16.N-(3-(3-Ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-23)

2-(1-(7-(3-Aminophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(SB1-E-23-1)

The mixture of SB1-E-21-6 (1.1 g, 3.82 mmol), SM-23-1 (800 mg, 6.19mmol), KF (1.0 g, 17.2 mmol) and NMP (3 mL) was stirred at 168° C. for12 h, after completion, concentrated to remove the solvent, the residuewas purified by silica gel (PE/ethyl acetate=2/1, 1/1) to obtainSB1-E-23-1 (light brown solid, 1.0 g, yield 69%). LCMS (m/z): 381[M+H]⁺.

N-(3-(3-Ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-23)

To a solution of SB1-E-23-1 (150 mg, 0.394 mmol), DIPEA (0.7 mL) inCH₃CN (12 mL) was added the solution of acryloyl chloride (54 mg, 0.597mmol) in CH₃CN (2 mL) dropwise, the mixture was stirred at 0° C. for 3h. after completion, concentrated to remove the solvent, the residue waspurified by prep-TLC (DCM/MeOH=30/1) and prep-HPLC (C18 column,CH₃CN/H₂O, containing 0.05% NH₄HCO₃) to obtain SB1-E-23, also referredto herein as E-9 and E9 (off-white solid, 15 mg, yield 9%). HPLC: 98%(254 nm); LCMS (m/z): 435 [M+H]+; ¹H NMR (DMSO-d₆, 500 MHz): δ 10.23 (s,1H), 9.29 (s, 1H), 7.88 (s, 1H), 7.76 (s, 1H), 7.33-7.36 (m, 2H),7.16-7.19 (m, 1H), 6.45 (dd, J₁=17.2 Hz, J₂=10.0 Hz, 1H), 6.27 (d,J=17.2 Hz, 1H), 6.01 (s, 1H), 5.77 (d, J=10.0 Hz, 1H), 4.58 (m, 2H),4.26 (m, 1H), 3.34-3.38 (m, 1H), 2.87 (t, 1H), 2.54 (q, J=7.2 Hz, 2H),1.28-1.84 (m, 8H), 1.22 (t, J=7.6 Hz, 3H).

Example 17.N-(3-(5-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-21)

tert-Butyl (1r,4r)-4-aminocyclohexylcarbamate (SB1-E-21-1)

To a solution of SM-21-1 (2.0 g, 17.5 mmol) in MeOH (100 mL) was addedthe solution of (Boc)₂₀ (1.1 g, 5.04 mmol) in MeOH (60 mL) dropwise for30 min, the mixture was stirred at r.t overnight. After completion,concentrated to remove the solvent, the residue was added H₂O (50 mL),further stirred at r.t for 20 min, then filtered, the filtrate wasextracted with ethyl acetate (120 mL×2), the organic phase was washedwith brine (50 mL×2), dried with Na₂SO₄. Filtered, concentrated toremove the solvent to obtain SB1-E-21-1 (off-white solid, 900 mg, yield83%).

tert-Butyl (1r,4r)-4-(dimethylamino)cyclohexylcarbamate (SB1-E-21-2)

To a solution of SB1-E-21-1 (850 mg, 3.97 mmol) and HCHO (600 mg, 20.0mmol) in MeOH (30 mL) was added NaBH₃CN (1.1 g, 17.5 mmol), the mixturewas stirred at r.t overnight, after completion, concentrated to removethe solvent, the residue was extracted with ethyl acetate (100 mL×4),the organic phase was washed with brine (50 mL×2), dried with Na₂SO₄.Filtered, concentrated to remove the solvent, the residue was purifiedby silica gel (DCM/MeOH=10/1, 5/1) to obtain SB1-E-21-2 (light brownsolid, 800 mg, yield 83%). LCMS (m/z): 243 [M+H]⁺.

(1r,4r)—N1,N1-Dimethylcyclohexane-1,4-diamine (SB1-E-21-3)

The mixture of SB1-E-21-2 (350 mg, 1.44 mmol), DCM (3 mL) and TFA (3 mL)was stirred at r.t for 3 h, after completion, concentrated to remove thesolvent to get SB1-E-21-3 (light yellow sticky oil, 200 mg, yield 98%).LCMS (m/z): 143 [M+H]⁺.

3-Ethylpyrazolo[1,5-a]pyrimidine-5,7(4H,6H)-dione (SB1-E-21-4)

The mixture of SM-21-2 (5.0 g, 24.8 mmol), dimethyl malonate (10 mL,87.0 mmol), MeOH (80 mL) and NaOMe (7.0 g, 129.6 mmol) was stirred at65° C. overnight, after completion, concentrated to remove the solvent,the residue was added H₂O (10 mL), 2 M HCl to make PH<7, then filtered,the solid was washed with H₂O (50 mL), dried to obtain SB1-E-21-4 (lightyellow solid, 2.6 g, yield 58%). LCMS (m/z): 180 [M+H]⁺.

5,7-Dichloro-3-ethylpyrazolo[1,5-a]pyrimidine (SB1-E-21-5)

To a suspension of SB1-21-4 (2.6 g, 14.5 mmol) in CH₃CN (20 mL) wasadded N,N-dimethylaniline (3.6 g, 29.7 mmol), POCl₃ (11.5 g, 75.0 mmol)dropwise, the mixture was stirred at 85° C. overnight. After completion,cooled to 0° C., added H₂O (50 mL) to quench the reaction, filtered, thesolid was washed with H₂O (50 mL), dried to obtain SB1-E-21-5 (lightbrown solid, 2.7 g, 86%). LCMS (m/z): 216 [M+H]⁺

N1-(5-Chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)benzene-1,3-diamine(SB1-E-21-6)

The mixture of SB1-E-21-5 (2.6 g, 12.0 mmol), SM-21-3 (1.5 g, 13.9mmol), DIPEA (5 mL) and i-PrOH (30 mL) was stirred at 85° C. for 6 h,after completion, concentrated to remove the solvent, the residue waspurified by silica gel (DCM/MeOH=200/1) to obtain SB1-E-21-6 (brownsolid, 2.8 g, yield 81%). LCMS (m/z): 288 [M+H]⁺.

N7-(3-Aminophenyl)-N5-((1r,4r)-4-(dimethylamino)cyclohexyl)-3-ethylpyrazolo[1,5-a]pyrimidine-5,7-diamine(SB1-E-21-7)

The mixture of SB1-E-21-6 (400 mg, 1.39 mmol), SB1-E-21-3 (200 mg, 1.41mmol), KF (400 mg, 6.88 mmol) and NMP (1.5 mL) was stirred at 145° C.for 10 h in a sealed tube. After completion, concentrated to remove thesolvent, the residue was purified by prep-TLC (DCM/MeOH=6/1) to obtainSB1-E-21-7 (light brown solid, 160 mg, yield 29%). LCMS (m/z): 394[M+H]⁺.

N-(3-(5-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-21)

To a solution of SB1-E-21-7 (60 mg, 0.152 mmol) and DIPEA (0.3 mL) inCH₃CN (3 mL) was added acrylyl chloride (25 mg, 0.276 mmol) in CH₃CN (1mL) dropwise, the mixture was stirred at 0° C. for 3 h. aftercompletion, concentrated to remove the solvent, the residue was purifiedby prep-TLC (DCM/MeOH=10/1) and prep-HPLC (C18 column, CH₃CN/H₂O,containing 0.05% NH₄HCO₃) to obtain SB1-E-21, also referred to herein asE-21 and E21 (off-white solid, 7 mg, yield 10%). HPLC: 99% (254 nm);LCMS (m/z): 448 [M+H]⁺; ¹H NMR (DMSO-d₆, 500 MHz): δ 10.26 (s, 1H), 9.07(s, 1H), 7.69 (s, 2H), 7.54 (d, J=9.0 Hz, 1H), 7.36 (t, J=8.5 Hz, 1H),7.09 (d, J=7.0 Hz, 1H), 6.63 (d, J=7.0 Hz, 1H), 6.46 (dd, J₁=17.5 Hz,J₂=12.0 Hz, 1H), 6.28 (d, J=17.5 Hz, 1H), 5.78 (d, J=12.0 Hz, 1H), 5.62(s, 1H), 2.55 (m, 4H), 2.17 (s, 6H), 1.78-2.13 (m, 4H), 1.12-1.27 (m,8H).

Example 18.N-(3-(5-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-3-isopropylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-26)

N-(3-(5-((1r,4r)-4-(Dimethylamino)cyclohexylamino)-3-isopropylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(SB1-E-26)

To a solution of SB1-E-25-6 (70 mg, 0.172 mmol) and DIPEA (0.5 mL) inCH₃CN (5 mL) was added acrylyl chloride (30 mg, 0.331 mmol) in CH₃CN (1mL), the mixture was stirred at r.t for 15 h, after completion,concentrated to remove the solvent, the residue was purified by prep-TLC(DCM/MeOH=10/1) and prep-HPLC (C18 column, CH₃CN/H₂O, containing 0.05%NH₄HCO₃) to obtain SB1-E-26, also referred to herein as E-26 and E26(white solid, 12 mg, yield 15%). HPLC: 100% (254 nm); LCMS (m/z): 462[M+H]⁺; ¹H NMR (DMSO-d₆, 500 MHz): δ 10.26 (s, 1H), 9.06 (s, 1H), 7.70(s, 1H), 7.67 (s, H), 7.54 (d, J=6.5 Hz, 1H), 7.36 (t, J=6.5 Hz, 1H),7.08 (d, J=1.5 Hz, 1H), 6.62 (d, J=6.0 Hz, 1H), 6.45 (dd, J₁=16.0 Hz,J₂=9.5 Hz, 1H), 6.28 (d, J=16.0 Hz, 1H), 5.78 (d, J=9.5 Hz, 1H), 5.62(s, 1H), 3.00 (m, 1H), 2.18 (s, 7H), 2.06 (d, J=10.5 Hz, 1H), 1.80 (d,J=10.5 Hz, 1H), 1.12-1.29 (m, 11H).

Example 19.N-((1R,4s)-4-((3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-yl)amino)cyclohexyl)acrylamide(MFH-1-169-1)

(1s,4s)-N1-(5-chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)cyclohexane-1,4-diamine(MFH-1-153-1)

The mixture of SM-1-49-1 (300 mg, 1.388 mmol), SM-1-167-1 (182 mg, 1.6mmol), DIPEA (270 mg) and i-PrOH (8 mL) was stirred at 85° C. for 2 h.After completion, the solvent was removed and the residue was purifiedby silica gel (NH₃/MeOH (1.75N)/DCM=0-20%) to obtain MFH-1-153-1 (240 g,yield 59%). LCMS (m/z): 294 [M+H]⁺.

2-((S)-1-(7-((1s,4R)-4-aminocyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-159-1)

The mixture of MFH-1-153-1 (230 mg, 0.783 mmol), SM-1-49-3 (182 mg, 1.41mmol), KF (205 mg, 3.5235 mmol), K₂CO₃ (194 mg, 1.41 mmol) and NMP (2mL) was stirred at 170° C. for 48 h. After completion, the residue wasextracted with chloroform/i-propanol (4/1) and the organic phase waswashed with brine (50 mL×2) and dried with Na₂SO₄. The residue afterremoval of the solvent was purified by silica gel (NH₃/MeOH(1.75N)/DCM=0-20%) to obtain MFH-1-159-1 (50 mg, yield 16.5%). LCMS(m/z): 387 [M+H]⁺.

N-((1R,4s)-4-(3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)cyclohexyl)acrylamide(MFH-1-169-1)

To a solution of MFH-1-159-1 (25 mg, 0.06468 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (8 mg, 0.0841 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the solvent was removed and the residue was purified byprep-HPLC (C18 column, MeOH/H₂O, containing 0.05% TFA) to obtainMFH-1-169-1 (off-white solid, 4.8 mg, yield 16%). HPLC: 97% (254 nm);LCMS (m/z): 441 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ 7.97 (d, J=7.2 Hz, 1H),7.87 (s, 1H), 7.44 (s, 1H), 6.30 (dd, J=17.1, 10.2 Hz, 1H), 6.09 (dd,J=17.1, 2.1 Hz, 1H), 5.78 (s, 1H), 5.59 (dd, J=10.2, 2.1 Hz, 1H), 4.49(s, 1H), 4.15 (d, J=12.3 Hz, 1H), 3.98-3.79 (m, 3H), 3.08 (t, J=12.4 Hz,2H), 2.61-2.52 (m, 2H), 1.95 (dd, J=18.6, 10.5 Hz, 1H), 1.84 (dt,J=12.9, 7.4 Hz, 2H), 1.79-1.57 (m, 10H), 1.56-1.44 (m, 1H), 1.18 (t,J=7.5 Hz, 3H).

Example 20.N-((1S,4r)-4-((3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-yl)amino)cyclohexyl)acrylamide(MFH-1-175-1)

(1r,4r)-N1-(5-chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)cyclohexane-1,4-diamine(MFH-1-161-1)

The mixture of SM-1-49-1 (300 mg, 1.388 mmol), SM-1-175-1 (250 mg, 2.19mmol), DIPEA (270 mg) and i-PrOH (8 mL) was stirred at 85° C. for 1 h.After completion, the solvent was removed and the residue was purifiedby silica gel (NH₃/MeOH (1.75N)/DCM=0-20%) to obtain MFH-1-161-1 (230 g,yield 56%). LCMS (m/z): 294 [M+H]⁺.

2-((S)-1-(7-((1r,4S)-4-aminocyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-163-1)

The mixture of MFH-1-161-1 (230 mg, 0.783 mmol), SM-1-49-3 (182 mg, 1.41mmol), KF (205 mg, 3.5235 mmol), K₂CO₃ (194 mg, 1.41 mmol) and NMP (2mL) was stirred at 170° C. for 48 h. After completion, the residue wasextracted with chloroform and 2-propanol (4:1) and the organic phase waswashed with brine (50 mL×2) and dried with Na₂SO₄. The residue afterremoval of solvent was purified by silica gel (NH₃/MeOH(1.75N)/DCM=0-20%) to obtain MFH-1-163-1(30 mg, yield 10%). LCMS (m/z):387 [M+H]⁺.

N-((1S,4r)-4-(3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)cyclohexyl)acrylamide(MFH-1-175-1)

To a solution of MFH-1-163-1 (30 mg, 0.07762 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (9 mg, 0.101 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the solvent was removed and the residue was purified byprep-HPLC (C18 column, MeOH/H₂O, containing 0.05% TFA) to obtainMFH-1-175-1 (off-white solid, 12.8 mg, yield 37%). HPLC: 97% (254 nm);LCMS (m/z): 441 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ 8.03 (d, J=7.5 Hz, 1H),7.90 (s, 1H), 6.24 (dd, J=17.1, 10.1 Hz, 1H), 6.08 (dd, J=17.1, 2.2 Hz,1H), 5.77 (d, J=10.8 Hz, 1H), 5.58 (dd, J=10.1, 2.3 Hz, 1H), 4.49 (s,1H), 4.14 (d, J=12.4 Hz, 2H), 3.74 (s, 2H), 3.62-3.49 (m, 2H), 3.43-3.34(m, 1H), 3.11 (t, J=13.0 Hz, 1H), 2.57 (dt, J=9.8, 4.9 Hz, 2H),2.07-1.82 (m, 5H), 1.83-1.56 (m, 8H), 1.53 (d, J=11.8 Hz, 1H), 1.39 (td,J=12.9, 3.6 Hz, 2H), 1.25-1.13 (m, 3H).

Example 21.(S)—N-(4-((3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-yl)amino)phenyl)acrylamide(MFH-1-187-1)

tert-butyl4-(5-chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenylcarbamate(MFH-1-177-1)

The mixture of SM-1-49-1 (500 mg, 2.314 mmol), SM-1-187-1 (520 mg, 2.5mmol), DIPEA (898 mg) and i-PrOH (8 mL) was stirred at 85° C. for 6 h.After completion, the solvent was removed and the residue was purifiedby silica gel chromatography (MeOH/DCM=0-20%) to obtain MFH-1-177-1 (898g, yield 100%). LCMS (m/z): 388 [M+H]⁺.

(S)-2-(1-(7-(4-aminophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-183-1)

The mixture of MFH-1-177-1 (449 mg, 1.157 mmol), SM-1-49-3 (240 mg,1.8512 mmol), KF (303 mg, 5.2 mmol) and NMP (2 mL) was stirred at 170°C. for 10 h. After completion, the solution was extracted withchloroform and 2-propanol (4:1) and the organic phase was washed withbrine (50 mL×2) and dried with Na₂SO₄. The solvent was removed and theresidue was purified by silica gel chromatography (MeOH/DCM=0-20%) toobtain MFH-1-183-1(400 mg, yield 91%). LCMS (m/z): 381 [M+H]⁺.

(S)—N-(4-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-1-187-1)

To a solution of MFH-1-183-1 (80 mg, 0.21 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (25 mg, 0.273 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the solvent was removed and the residue was purified byprep-HPLC (C18 column, MeOH/H₂O, containing 0.05% TFA) to obtainMFH-1-187-1 (off-white solid, 33.6 mg, yield 36.8%). HPLC: 96% (254 nm);LCMS (m/z): 435 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ 10.26 (s, 1H), 9.83 (s,1H), 7.91 (s, 1H), 7.76 (t, J=13.5 Hz, 2H), 7.42 (d, J=8.9 Hz, 2H), 6.46(dd, J=17.0, 10.1 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.84-5.68 (m,2H), 4.42 (s, 1H), 4.02 (s, 2H), 3.32 (ddd, J=10.9, 8.2, 4.9 Hz, 2H),3.00 (dd, J=24.6, 11.8 Hz, 1H), 2.64-2.55 (m, 2H), 1.90 (td, J=13.5, 5.1Hz, 1H), 1.76-1.51 (m, 6H), 1.49-1.33 (m, 1H), 1.27-1.17 (m, 3H).

Example 22.N-(3-(((2-(((1r,4r)-4-(dimethylamino)cyclohexyl)amino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-yl)amino)methyl)phenyl)acrylamide(MFH-2-67-1)

tert-butyl (1r,4r)-4-aminocyclohexylcarbamate (MFH-2-61-1)

To a solution of SM-2-67-1 (2.0 g, 17.5 mmol) in MeOH (100 mL) was addedthe solution of (Boc)₂₀ (1.1 g, 5.04 mmol) in MeOH (60 mL) dropwise for30 min. The mixture was stirred at room temperature overnight. Aftercompletion, the solvent was removed and to the residue was added H₂O (50mL) and further stirred at room temperature for 20 min and thenfiltered. The filtrate was extracted with ethyl acetate (120 mL×2) andthe organic phase was washed with brine (50 mL×2) and dried with Na₂SO₄.The solution was then concentrated under reduced pressure to obtainMFH-2-61-1 (off-white solid, 900 mg, yield 83%).

tert-butyl (1r,4r)-4-(dimethylamino)cyclohexylcarbamate (MFH-2-62-1)

To a solution of MFH-2-61-1 (850 mg, 3.97 mmol) and HCHO (600 mg, 20.0mmol) in MeOH (30 mL) was added NaBH₃CN (1.1 g, 17.5 mmol) and themixture was stirred at room temperature overnight. After completion, thesolvent was removed and the residue was extracted with ethyl acetate(100 mL×4) and the organic phase was washed with brine (50 mL×2) anddried with Na₂SO₄. The residue after removal of solvent was purified bysilica gel chromatography (DCM/MeOH=10/1, 5/1) to obtain MFH-2-62-1(light brown solid, 800 mg, yield 83%). LCMS (m/z): 243 [M+H]⁺.

(1r,4r)—N1,N1-dimethylcyclohexane-1,4-diamine (MFH-2-64-1)

To a mixture of compound MFH-2-62-1 (350 mg, 1.44 mmol) in methanol (5mL) was added 4N HCl/dioxane (10 mL) and stirred for 3h at roomtemperature. The mixture was concentrated and the crude mixture wasdirectly used in the next step. LCMS (m/z): 143 [M+H]⁺.

tert-butyl3-((8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)methyl)phenylcarbamate(MFH-2-55-1)

A stirred mixture of MFH-2-34-1 (220 mg, 0.962 mmol), tert-butyl3-(aminomethyl) phenylcarbamate (214 mg, 0.962 mmol) and NaHCO₃ (121 mg,1.443 mmol) in acetonitrile (5 mL) was heated at 75° C. overnight andthen was cooled to room temperature. The solution was filtered andconcentrated under reduced pressure. The residue was purified by silicagel chromatography (PE/ethyl acetate=3:1 to 1:1) to afford MFH-2-55-1(white solid, 210 mg, yield: 52%). LCMS (m/z): 415 [M+H]⁺.

tert-butyl3-((8-ethyl-2-(methylsulfonyl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)methyl)phenylcarbamate(MFH-2-65-1)

To a solution of MFH-2-55-1 (110 mg, 0.2654 mmol) in DCM (3 mL) wasadded 3-chloroperbenzoic acid (137 mg, 0.7961 mmol) in one portion atroom temperature and was stirred at for 1 h. The reaction mixture wasquenched with a saturated Na₂S₂O₃ solution (10 mL), diluted with DCM (50mL), washed with saturated aqueous NaCl (3×50 mL), dried over anhydrousNa₂SO₄, filtered, and concentrated to give MFH-2-65-1 (yellow solid, 118mg, yield: 100%), which was used in next step directly. LCMS (m/z): 447[M+H]⁺.

N4-(3-aminobenzyl)-N2-((1r,4r)-4-(dimethylamino)cyclohexyl)-8-ethylpyrazolo[1,5-a][1,3,5]triazine-2,4-diamine(MFH-2-66-1)

To a stirred mixture MFH-2-65-1 (118 mg, 0.2654 mmol) and MFH-2-64-1 (98mg, 0.4554 mmol) in N-methyl-2-pyrrolidone (3 mL) was added KF (46 mg,0.7962 mmol). This mixture was heated at 170° C. for 3 h and then wascooled and filtered. The crude mixture was purified by silica gelchromatography (MeOH/DCM=0-20%) to afford MFH-2-66-1 (yellow solid, 30mg, yield: 28%). LCMS (m/z): 409 [M+H]⁺.

N-(3-((2-((1r,4r)-4-(dimethylamino)cyclohexylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-ylamino)methyl)phenyl)acrylamide(MFH-2-67-1)

To a solution of MFH-2-66-1 (30 mg, 0.07343 mmol) in CH₃CN (2 mL) wereadded acryloyl chloride (9 mg, 0.1 mmol) and DIPEA (0.2 mL). Thereaction was stirred at room temperature for 2 h. After completion, thereaction mixture was diluted with dichloromethane (10 ml), washed withwater (10 mL) and a saturated sodium bicarbonate solution (10 mL×2), anddried over anhydrous sodium sulfate. The residue after removal of thesolvent was purified by prep-HPLC (C18 column, MeOH/H₂O, containing0.05% TFA) to obtain MFH-2-67-1 (off-white solid, 11.3 mg, yield 28%).HPLC: 97% (254 nm); LCMS (m/z): 463 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ10.16 (s, 1H), 9.81 (s, 1H), 9.53 (s, 1H), 8.75 (s, 1H), 7.95 (d, J=40.1Hz, 1H), 7.77 (s, 1H), 7.64-7.48 (m, 1H), 7.30 (s, 1H), 6.42 (dd,J=16.9, 10.1 Hz, 1H), 6.31-6.14 (m, 1H), 5.75 (d, J=11.4 Hz, 1H), 4.64(d, J=6.1 Hz, 2H), 3.17 (d, J=8.6 Hz, 2H), 2.94-2.56 (m, 6H), 2.48 (s,1H), 1.99 (dd, J=87.3, 31.8 Hz, 4H), 1.51 (s, 2H), 1.39-0.96 (m, 6H).

Example 23.N-(3-((2-(((1r,4r)-4-(dimethylamino)cyclohexyl)amino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-yl)amino)cyclohexyl)acrylamide(MFH-2-78-1)

N1-(8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-yl)cyclohexane-1,3-diamine(MFH-2-56-1)

MFH-2-34-1 (220 mg, 0.96 mmol) and cyclohexane-1,3-diamine (330 mg, 2.88mmol) were dissolved in acetonitrile (5 mL). The mixture was heated at75° C. overnight. The solvent was then removed under reduced pressure.The crude mixture was purified by silica gel chromatography (NH₃/MeOH(1.75N)/DCM=0-20%) to obtain MFH-2-56-1 (white solid, 193 mg, yield:65%). LCMS (m/z): 307 [M+H]⁺.

tert-butyl3-(8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)cyclohexylcarbamate(MFH-2-58-1)

To a solution of MFH-2-56-1 (193 mg, 0.63 mmol) in MeOH (6 mL) was addeddi-tert-butyl dicarbonate (206 mg, 0.94 mmol) and TEA (191 mg 1.89mmol). The reaction mixture was stirred at room temperature overnight.The reaction mixture was concentrated under reduced pressure to affordthe residue, which was purified by flash column chromatography(MeOH/DCM=0-20%) to afford MFH-2-58-1 (210 mg, yield: 82%). LCMS (m/z):407 [M+H]⁺.

tert-butyl3-(8-ethyl-2-(methylsulfonyl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)cyclohexylcarbamate(MFH-2-69-1)

To a solution of MFH-2-58-1 (210 mg, 0.51 mmol) in DCM (5 mL) was added3-chloroperbenzoic acid (268 mg, 1.55 mmol). The mixture was stirred atroom temperature for 1 h and then was quenched with a saturated Na₂S₂O₃solution (5 mL). The reaction mixture was extracted with DCM (50 mL) andthe organic layer was washed with saturated aqueous NaCl (3×50 mL),dried over anhydrous Na₂SO₄, filtered and concentrated to giveMFH-2-69-1 (226.6 mg, yield: 100%) as the crude product, which was usedfor next step directly. LCMS (m/z): 439 [M+H]⁺.

tert-butyl3-(2-((1r,4r)-4-(dimethylamino)cyclohexylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-ylamino)cyclohexylcarbamate(MFH-2-70-1)

To a stirred mixture MFH-2-69-1 (226.6 mg, 0.51 mmol) and MFH-2-64-1(118 mg, 0.83 mmol) in N-methyl-2-pyrrolidone (3 mL) was added KF (90mg, 1.551 mmol). This mixture was heated at 170° C. for 3 h, and thencooled and filtered. The crude mixture was then purified by silica gelchromatography (NH₃/MeOH (1.75N)/DCM=0-20%) to afford MFH-2-70-1 (120mg, yield: 47%). LCMS (m/z): 501 [M+H]⁺.

N4-(3-aminocyclohexyl)-N2-((1r,4r)-4-(dimethylamino)cyclohexyl)-8-ethylpyrazolo[1,5-a][1,3,5]triazine-2,4-diamine(MFH-2-77-1)

To a mixture of compound MFH-2-70-1 (60 mg, xx mmol) in methanol (5 mL)was added 4N HCl/dioxane (5 mL) and the solution was stirred for 3h atroom temperature. The mixture was concentrated under reduced pressureand the crude mixture was directly used in next step. LCMS (m/z): 401[M+H]⁺.

N-(3-(2-((1r,4r)-4-(dimethylamino)cyclohexylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-4-ylamino)cyclohexyl)acrylamide(MFH-2-78-1)

To a solution of MFH-2-77-1 (48 mg, 0.12 mmol) in CH₃CN (2 mL) was addedacryloyl chloride (14 mg, 0.156 mmol) and DIPEA (0.2 ml). The reactionmixture was stirred at room temperature for 2 h. After completion, thereaction mixture was diluted with dichloromethane (10 ml), washed with asaturated NaHCO₃ solution (10 mL×2), and washed with water (10 mL). Theorganic layer was dried over anhydrous sodium sulfate, concentratedunder reduced pressure and the residue was purified by prep-HPLC (C18column, MeOH/H₂O, containing 0.05% TFA) to afford MFH-2-78-1 (whitesolid, 25.2 mg, yield: 46%). HPLC: 97% (254 nm); LCMS (m/z): 455 [M+H]⁺;¹H NMR (500 MHz, DMSO) δ 9.51 (s, 1H), 8.15 (s, 1H), 7.92 (s, 1H), 7.74(s, 1H), 6.20 (dd, J=16.9, 9.9 Hz, 1H), 6.15-6.03 (m, 1H), 5.58 (d,J=9.8 Hz, 1H), 3.17 (s, 3H), 2.75 (d, J=4.9 Hz, 6H), 2.49 (d, J=2.3 Hz,1H), 2.47 (dd, J=7.5, 2.1 Hz, 1H), 2.23-1.91 (m, 5H), 1.90-1.71 (m, 3H),1.45 (ddd, J=45.3, 44.9, 21.3 Hz, 8H), 1.15 (s, 4H).

Example 24.(S)—N-(3-(((3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-yl)amino)methyl)phenyl)acrylamide(MFH-1-49-1)

tert-butyl-3-((5-chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)methyl)phenylcarbamate(MFH-1-39-1)

The mixture of SM-1-49-1 (400 mg, 1.85 mmol), SM-1-49-2 (452.6 mg,2.0364 mmol), DIPEA (718 mg) and i-PrOH (5 mL) was stirred at 85° C. for6 h. Then the reaction mixture was concentrated under reduced pressureand the residue was purified by silica gel chromatography (PE/EA=0-50%)to obtain MFH-1-39-1 (white solid, 0.66 g, yield 88.7%). LCMS (m/z): 402[M+H]⁺.

(S)-2-(1-(7-(3-aminobenzylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-43-1)

The mixture of MFH-1-39-1 (660 mg, 1.6422 mmol), SM-1-49-3 (318 mg,2.4633 mmol), KF (429 mg, 7.4 mmol) and NMP (2 mL) was stirred at 170°C. for 10 h. After completion, the residue was extracted with chloroformand isopropanol (4:1) and the organic phase was washed with brine (50mL×2) and dried with Na₂SO₄. The solution was filtered and concentratedunder reduced pressure. The residue was purified by silica gelchromatography (MeOH/DCM=0-20%) to obtain MFH-1-43-1 (396.3 mg, yield61%). LCMS (m/z): 395 [M+H]⁺.

(S)—N-(3-((3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)methyl)phenyl)acrylamide(MFH-1-49-1)

To a solution of MFH-1-43-1 (60 mg, 0.15 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (18 mg, 0.20 mmol) in DCM (0.5mL) dropwise. The mixture was then stirred at 0° C. for 1 h. Afterreaction completion, the reaction was concentrated to remove the solventand the residue was purified by prep-HPLC (C18 column, MeOH/H₂O,containing 0.05% TFA) to obtain MFH-1-49-1 (off-white solid, 8.6 mg,yield 12.6%). HPLC: 96% (254 nm); LCMS (m/z): 449 [M+H]⁺; ¹H NMR (500MHz, DMSO) δ 10.14 (s, 1H), 8.94 (s, 1H), 7.91 (s, 1H), 7.72 (s, 1H),7.53 (d, J=8.1 Hz, 1H), 7.30 (t, J=7.8 Hz, 1H), 7.13 (d, J=7.6 Hz, 1H),6.41 (dd, J=17.0, 10.1 Hz, 1H), 6.22 (dd, J=17.0, 1.7 Hz, 1H), 5.73 (dd,J=10.1, 1.7 Hz, 1H), 5.66 (s, 1H), 4.62 (d, J=6.3 Hz, 2H), 4.41 (s, 1H),3.96 (d, J=11.7 Hz, 2H), 3.06 (t, J=12.6 Hz, 1H), 2.60-2.51 (m, 2H),1.96 (d, J=5.0 Hz, 1H), 1.73-1.58 (m, 5H), 1.53 (s, 1H), 1.43 (d, J=11.6Hz, 2H), 1.12 (t, J=7.5 Hz, 3H), 1.08 (s, 1H).

Example 25(R)—N-(3-((3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)methyl)phenyl)acrylamide(MFH-1-56-1)

(R)-2-(1-(7-(3-aminobenzylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-47-1)

The mixture of MFH-1-39-1 (330 mg, 0.8211 mmol), SM-1-56-1 (248.6 mg,1.3884 mmol), KF (242 mg, 4.1652 mmol) and NMP (1 mL) was stirred at170° C. for 10 h. After completion, the residue was extracted withchloroform and 2-propanol (4:1). The organic phase was washed with brine(50 mL×2) and dried with Na₂SO₄. The solvent was removed and the residuewas purified by silica gel chromatography (MeOH/DCM=0-20%) to obtainMFH-1-56-1 (259 mg, yield 80%). LCMS (m/z): 395 [M+H]⁺.

(R)—N-(3-((3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)methyl)phenyl)acrylamide(MFH-1-56-1)

To a solution of MFH-1-47-1 (60 mg, 0.152 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (18 mg, 0.198 mmol) in DCM (0.5mL) dropwise. The mixture was then stirred at 0° C. for 1 h. Aftercompletion, the solution was concentrated and the residue was purifiedby prep-HPLC (C18 column, MeOH/H₂O, containing 0.05% TFA) to obtainMFH-1-56-1 (off-white solid, 10 mg, yield 14.6%). HPLC: 98% (254 nm);LCMS (m/z): 449 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ 10.16 (s, 1H), 9.04 (s,1H), 7.93 (s, 1H), 7.76 (s, 1H), 7.54 (d, J=8.1 Hz, 1H), 7.31 (t, J=7.8Hz, 1H), 7.14 (d, J=7.6 Hz, 1H), 6.42 (dd, J=17.0, 10.1 Hz, 1H), 6.24(dd, J=17.0, 1.7 Hz, 1H), 5.75 (dd, J=10.1, 1.7 Hz, 1H), 5.68 (s, 1H),4.65 (d, J=6.3 Hz, 2H), 4.42 (s, 1H), 3.98 (d, J=11.7 Hz, 2H), 3.09 (t,J=12.6 Hz, 1H), 2.61-2.54 (m, 2H), 1.96 (d, J=5.0 Hz, 1H), 1.76-1.60 (m,5H), 1.58 (s, 1H), 1.44 (d, J=11.6 Hz, 2H), 1.19 (t, J=7.5 Hz, 3H), 1.10(s, 1H).

Example 26(R)—N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-1-143-1)

(R)-2-(1-(7-(3-aminophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-121-1)

The mixture of SM-1-141-1 (250 mg, 0.869 mmol), SM-1-56-3 (168 mg, 1.3mmol), KF (227 mg, 3.9 mmol) and NMP (2 mL) was stirred at 170° C. for10 h. After completion, the residue was extracted with chloroform and2-propanol (4:1). The organic phase was washed with brine (50 mL×2) anddried with Na₂SO₄. The solvent was removed and the residue was purifiedby silica gel chromatography (MeOH/DCM=0-20%) to obtain MFH-1-43-1(220mg, yield 66.5%). LCMS (m/z): 381 [M+H]⁺.

(R)—N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-1-143-1)

To a solution of MFH-1-121-1 (50 mg, 0.13141 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (15 mg, 0.17 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the solvent was removed and the residue was purified byprep-HPLC (C18 column, MeOH/H₂O, containing 0.05% TFA) to obtainMFH-1-143-1 (off-white solid, 18 mg, yield 31.5%). HPLC: 96% (254 nm);LCMS (m/z): 435 [M+H]+; ¹H NMR (500 MHz, DMSO) δ 10.29 (s, 1H), 9.89 (s,1H), 7.92 (d, J=11.7 Hz, 2H), 7.43-7.34 (m, 2H), 7.24-7.15 (m, 1H), 6.46(dd, J=17.0, 10.1 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.94 (s, 1H),5.79 (dd, J=10.1, 1.9 Hz, 1H), 4.51 (s, 1H), 4.07 (s, 1H), 3.48-3.40 (m,2H), 3.35-3.31 (m, 1H), 3.02 (t, J=12.8 Hz, 1H), 2.63-2.55 (m, 2H), 1.92(td, J=13.6, 5.2 Hz, 1H), 1.76-1.60 (m, 5H), 1.58 (s, 1H), 1.44 (d,J=11.9 Hz, 1H), 1.28-1.08 (m, 4H).

Example 27N-(3-(3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)cyclohexyl)acrylamide(MFH-1-167-1)

N1-(5-chloro-3-ethylpyrazolo[1,5-a]pyrimidin-7-yl)cyclohexane-1,3-diamine(MFH-1-151-1)

The mixture of SM-1-49-1 (300 mg, 1.388 mmol), SM-1-167-1 (500 mg, 4.442mmol), DIPEA (270 mg) and i-PrOH (5 mL) was stirred at 85° C. for 2 h.After completion, the reaction was concentrated to remove the solventand the residue was purified by silica gel (NH₃/MeOH (1.75N)/DCM=0-20%)to obtain MFH-1-155-1 (230 g, yield 56%). LCMS (m/z): 294 [M+H]⁺.

2-((S)-1-(7-(3-aminocyclohexylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-157-1)

The mixture of MFH-1-155-1 (230 mg, 0.783 mmol), SM-1-49-3 (152 mg,1.1745 mmol), KF (205 mg, 3.5235 mmol) and NMP (2 mL) was stirred at170° C. for 10 h. After completion, the residue was extracted withchloroform and 2-propanol (4:1), the organic phase was washed with brine(50 mL×2), and dried with Na₂SO₄. The solution was filtered,concentrated to remove the solvent, and the residue was purified bysilica gel chromatography (NH₃/MeOH (1.75N)/DCM=0-20%) to obtainMFH-1-157-1(100 mg, yield 33%). LCMS (m/z): 387 [M+H]⁺.

N-(3-(3-ethyl-5-((S)-2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)cyclohexyl)acrylamide(MFH-1-167-1)

To a solution of MFH-1-157-1 (30 mg, 0.07762 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acrylyl chloride (9 mg, 0.101 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the reaction was concentrated to remove the solvent and theresidue was purified by prep-HPLC (C18 column, MeOH/H₂O, containing0.05% TFA) to obtain MFH-1-167-1 (off-white solid, 13 mg, yield 38%).HPLC: 96% (254 nm); LCMS (m/z): 441 [M+H]⁺; ¹H NMR (500 MHz, DMSO) δ8.26 (s, 1H), 8.14 (dd, J=18.8, 7.9 Hz, 1H), 8.05 (d, J=7.3 Hz, 1H),7.97-7.83 (m, 2H), 6.41-6.29 (m, 1H), 6.21 (ddd, J=17.1, 10.1, 2.0 Hz,1H), 6.09 (dddd, J=12.3, 10.2, 3.9, 2.2 Hz, 2H), 5.83 (d, J=9.4 Hz, 1H),5.69-5.51 (m, 3H), 4.49 (s, 2H), 4.12 (d, J=4.8 Hz, 2H), 3.88-3.81 (m,2H), 3.11 (dd, J=22.2, 12.4 Hz, 2H), 2.60-2.56 (m, 2H), 2.01-1.96 (m,2H), 1.69 (d, J=12.3 Hz, 6H), 1.54 (s, 2H), 1.48 (d, J=11.4 Hz, 2H),1.10 (dd, J=24.9, 12.8 Hz, 1H).

Example 28(S)—N-(3-(8-ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(MFH-2-53-1)

ethyl N-[(4-ethyl-1H-pyrazol-5-yl)carbamothioyl]carbamate (MFH-1-113-1)

To a solution of SM-2-53-1 (2.8 g, 25.2 mmol) in ethanol (50.0 mL) wasadded ethoxycarbonyl isothiocyanate (3.3 g, 25.2 mL) in one portion atroom temperature. The mixture was stirred at 80° C. overnight. Thereaction mixture was concentrated under reduced pressure to afford theresidue, which was purified by flash column chromatography (PE/ethylacetate=3:1) to afford MFH-1-113-1 (white solid, 4 g, yield: 65%). LCMS(m/z): 243 [M+H]⁺.

8-ethyl-2-thioxo-2,3-dihydropyrazolo[1,5-a][1,3,5]triazin-4(1H)-one(MFH-1-135-1)

To a solution of MFH-1-113-1 (3.9 g, 16.1 mmol) in acetonitrile (40 mL)was added K₂CO₃ (6.67 g, 48.3 mmol) in one portion at room temperature.The mixture was heated at 85° C. overnight, cooled, and then acidifiedwith AcOH. The resulting solid was filtered off to afford MFH-1-135-1(yellow solid, 2.1 g, yield: 66%). LCMS (m/z): 197 [M+H]⁺.

8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4(3H)-one(MFH-1-149-1)

To a stirred mixture of MFH-1-135-1 (2.1 g, 10.7 mmol) and NaOH (0.86 g,21.4 mmol) in dioxane/H₂O (30/8 mL) was added iodomethane (1.52 g, 10.7mol). This mixture was stirred at room temperature for 1 h, acidifiedwith hydrochloric acid, concentrated to remove the solvent, and theresidue was purified by silica gel chromatography (DCM/MeOH=30:1) toafford MFH-1-149-1 (white solid, 2.0 g, yield: 89%). LCMS (m/z): 211[M+H]⁺.

4-chloro-8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazine(MFH-2-34-1)

To a stirred mixture MFH-1-149-1 (2.0 g, 9.5 mmol) and N,N-dimethylaniline (2.3 g, 19.0 mmol) in acetonitrile (10 mL) under argon was addedPOCl₃ (20 ml, 219 mol). This mixture was heated at 85° C. overnight.Then the reaction mixture was concentrated under reduced pressure toafford the residue MFH-2-34-1 (white solid, 2.2 g, yield: 100% used nextstep directly). LCMS (m/z): 229 [M+H]⁺.

tert-butyl3-(8-ethyl-2-(methylthio)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenylcarbamate(MFH-2-45-1)

A stirred mixture MFH-2-34-1 (2.2 g, 9.5 mmol), tert-butyl3-aminophenylcarbamate (2.37 g, 11.4 mmol) and NaHCO₃ (130.4 mg, 0.95mmol) in acetonitrile (25 mL) was heated at 75° C. overnight and thencooled to room temperature. The solvent was removed and the residue waspurified by silica gel chromatography (PE/ethyl acetate=3/1 to 1/1) toafford MFH-2-45-1 (white solid, 2.52 g, yield: 67%). LCMS (m/z): 401[M+H]⁺.

tert-butyl3-(8-ethyl-2-(methylsulfonyl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenylcarbamate (MFH-2-50-1)

To a solution of MFH-2-45-1 (600 mg, 1.5 mmol) in DCM (15 mL) was added3-chloroperbenzoic acid (776 mg, 4.5 mmol) in one portion at roomtemperature and stirred for 1 h. The reaction mixture was quenched witha saturated Na₂S₂O₃ solution (10 mL), diluted with DCM (50 mL), washedwith saturated aqueous NaCl (3×50 mL), dried over anhydrous Na₂SO₄,filtered and concentrated to give MFH-2-50-1 (yellow solid, 620 mg,yield: 96%), which was used in the next step directly. LCMS (m/z): 433[M+H]⁺.

(S)-2-(1-(4-(3-aminophenylamino)-8-ethylpyrazolo[1,5-a][1,3,5]triazin-2-yl)piperidin-2-yl)ethanol(MFH-2-51-1)

To a stirred mixture of MFH-2-50-1 (360 mg, 0.84 mmol) and(S)-2-(piperidin-2-yl)ethanol (215 mg, 1.67 mmol) inN-methyl-2-pyrrolidone (3 mL) was added KF (146 mg, 2.51 mmol). Thismixture was heated at 170° C. for 3 h, cooled, and filtered. The crudemixture was purified by silica gel chromatography (MeOH/DCM=0-20%) toafford MFH-2-51-1 (yellow solid, 150 mg, yield: 47%). LCMS (m/z): 382[M+H]⁺.

(S)—N-(3-(8-ethyl-2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a][1,3,5]triazin-4-ylamino)phenyl)acrylamide(MFH-2-53-1)

To a solution of MFH-2-51-1 (70 mg, 0.18 mmol) in THF (2 mL) were addedacryloyl chloride (18 mg, 0.20 mmol) and triethylamine (54 mg, 0.54mmol). The reaction was stirred at room temperature for 2 h. Aftercompletion, the reaction mixture was diluted with dichloromethane (10ml), washed with water (10 mL) and saturated sodium bicarbonate solution(10 mL×2), dried over anhydrous sodium sulfate, concentrated and thecrude mixture was purified by prep-HPLC (C18 column, MeOH/H₂O,containing 0.05% TFA) to afford MFH-2-53-1 (white solid, 13 mg, yield:16%). HPLC: 97% (254 nm); LCMS (m/z): 436 [M+H]⁺; ¹H NMR (DMSO-d₆, 500MHz): δ: 10.17 (s, 1H), 10.07 (s, 1H), 8.34 (s, 1H), 7.84 (s, 1H), 7.51(s, 1H), 7.30-7.34 (m, 2H), 6.46 (dd, J=17, 10.0 Hz, 1H), 6.28 (d, J=17Hz, 1H), 5.77 (d, J=11.5 Hz, 1H), 4.98 (s, 1H), 4.65 (d, J=13 Hz, 1H),4.56 (s, 1H), 2.88 (t, J=12.5 Hz, 1H), 2.47-2.50 (m, 2H), 1.56-1.88 (m,8H), 1.36-1.38 (m, 1H), 1.19-1.23 (m, 4H).

Example 29N-(3-(5-(3-aminopiperidin-1-yl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-3-140-1)

tert-butyl1-(7-(3-aminophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-3-ylcarbamate(MFH-3-130-1)

To a stirred mixture SM-1-141-1 (150 mg, 0.5213 mmol) and SM-3-140-1(157 mg, 0.782 mmol) in N-methyl-2-pyrrolidone (1 mL) was added KF (136mg, 2.3458 mmol). After heating at 150° C. for 10 h, the reactionmixture was cooled and filtered. After removal of the solvent, the crudemixture was purified by silica gel chromatography (MeOH/DCM=0-20%) toafford MFH-3-130-1 (110 mg, yield: 47%). LCMS (m/z): 452 [M+H]⁺.

tert-butyl1-(7-(3-acrylamidophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-3-ylcarbamate(MFH-3-139-1)

To a solution of MFH-3-130-1 (110 mg, 0.24 mmol) in CH₃CN (2 mL) wasadded acryloyl chloride (28 mg, 0.3167 mmol) and DIPEA (0.2 ml). Thereaction was stirred at room temperature for 2 h and then was dilutedwith dichloromethane (10 ml). The solution was washed with saturatedNaHCO₃ (10 mL×2) and water (10 mL). The organic layer was dried overanhydrous sodium sulfate and then concentrated under reduced pressure.The residue was purified by prep-HPLC (C18 column, MeOH/H₂O, containing0.05% TFA) to afford MFH-3-139-1 (56.6 mg, yield: 46%). LCMS (m/z): 506[M+H]⁺.

N-(3-(5-(3-aminopiperidin-1-yl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-3-140-1)

To a mixture of compound MFH-3-139-1 (56.6 mg) in DCM (5 mL) was addedTFA (2 mL). The reaction mixture was stirred for 1 h at roomtemperature. The mixture was concentrated under reduced pressure and theresidue was purified by prep-HPLC (C18 column, MeOH/H₂O, containing0.05% TFA) to afford MFH-3-140-1 (20 mg, yield: 44%). LCMS (m/z): 406[M+H]⁺. ¹H NMR (500 MHz, DMSO) δ 10.32 (s, 1H), 9.48 (s, 1H), 7.97 (d,J=8.0 Hz, 1H), 7.94 (s, 2H), 7.84 (s, 1H), 7.38 (t, J=8.0 Hz, 1H), 7.32(d, J=8.2 Hz, 1H), 7.17 (d, J=8.6 Hz, 1H), 6.46 (dd, J=17.0, 10.2 Hz,1H), 6.28 (dd, J=17.0, 1.8 Hz, 1H), 6.03 (s, 1H), 5.80 (dd, J=10.1, 1.8Hz, 1H), 4.30 (s, 1H), 3.85 (s, 1H), 3.22 (s, 1H), 3.13 (dd, J=12.6, 9.2Hz, 2H), 2.66-2.57 (m, 2H), 1.98 (s, 1H), 1.81-1.74 (m, 1H), 1.56 (dd,J=16.8, 9.0 Hz, 2H), 1.25 (t, J=7.5 Hz, 3H).

Example 30(S)—N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-1-141-1)

(S)-2-(1-(7-(3-aminophenylamino)-3-ethylpyrazolo[1,5-a]pyrimidin-5-yl)piperidin-2-yl)ethanol(MFH-1-119-1)

The mixture of SM-1-141-1 (250 mg, 0.87 mmol), SM-1-49-3 (168 mg, 1.3mmol), KF (227 mg, 3.9 mmol) and NMP (2 mL) was stirred at 170° C. for10 h. After completion, the residue was extracted with chloroform andisopropanol (4:1). The organic phase was washed with brine (50 mL×2) anddried with Na₂SO₄. The mixture was filtered, concentrated to remove thesolvent under reduced pressure, and purified by silica gelchromatography (MeOH/DCM=0-20%) to obtain MFH-1-43-1(250 mg, yield75.6%). LCMS (m/z): 381 [M+H]⁺.

(S)—N-(3-(3-ethyl-5-(2-(2-hydroxyethyl)piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7-ylamino)phenyl)acrylamide(MFH-1-141-1)

To a solution of MFH-1-119-1 (50 mg, 0.13 mmol) and DIPEA (0.2 mL) inCH₃CN (2 mL) was added acryloyl chloride (15 mg, 0.17 mmol) in DCM (0.5mL) dropwise. The mixture was stirred at 0° C. for 1 h. Aftercompletion, the reaction was concentrated under reduced pressure, andthe residue was purified by prep-HPLC (C18 column, MeOH/H₂O, containing0.05% TFA) to obtain MFH-1-141-1 (off-white solid, 33.7 mg, yield 59%).HPLC: 96% (254 nm); LCMS (m/z): 435 [M+H]⁺.

Biological Assays of the Compounds

Pulldown Assay

Jurkat cells were treated with DMSO, 1 uM or 200 nM of compound E9, E17,or dinaciclib (FIG. 2). 6 hours after treatment, cells were washed andharvested by resuspending in lysis buffer (50 mM Hepes pH 7.4, 150 mMNaCl, 1% NP-40, 5 mM EDTA, protease and phosphatase inhibitors) andlysing on ice 30 minutes. Lysates were cleared by centrifugation at15,000 rpm 30 minutes. Biotin-labeled THZ1 was added to 1 uM to lysatesand rotated at 4° C. overnight. Streptavidin-agarose beads were washedand 30 uL slurry was added to each lysate and rotated for 1 hour at 4°C. Beads were washed 5 times with lysis buffer and 50 uL 2×LDS bufferwas added to each sample. Samples were boiled and equal volume ofprotein was loaded onto gel. Gel was transferred to nitrocellulose andblotted for Cyclin K and Cyclin H.

We conclude that pre-treatment of cells with compound E9, E17 ordinaciclib, but not DMSO, blocks biotin-THZ1 from being able to bind toCDK12, which blocks the pulldown of Cyclin K. This indicates thatcompound E9 is able to engage CDK12 in cells at 1 uM and 200 nM andblock binding of bio-THZ1. We do not see a similar loss of pulldown ofCyclin H, indicating that E9 and E17 are not able to bind to CDK7 andblock its association with bio-THZ1.

Jurkat Proliferation Assay

Jurkat cells were seeded at a density of 25,000 cells/well in 96-wellplates. Cells were then treated with the indicated compounds in a 10-ptdose escalation format from 1 nM to 10 μM or DMSO control for 72 hrs.After 72 hrs, cells were assayed using CellTiter-Glo Luminescent CellViability Assay (Promega) to determine cell viability by measuring theamount of ATP present in each sample cell population, which is anindicator of cell metabolic activity. Results are graphed as fraction ofthe DMSO control at 72 hrs. All data points were performed in biologicaltriplicate. Error bars are +/−SD.

These results suggest that dinaciclib has the most anti-proliferativeeffect on Jurkat cells with an IC50 below 10 nM. However, the covalentinhibitors E9, E17, and E18 all display potent activity with IC50s inthe sub-100 nM range.

Growth Assay

Jurkat cells were treated with 1 uM of compound E9, E17, Dinaciclib orDMSO control. 4 hours after treatment, cells were either not treated orwashed three times with RPMI media to remove all compound. Cells werereplated and allowed to grow for 68 hours. Cells were assayed usingcelltiter glo (Promega) to determine cell viability by measuring theamount of ATP present, which is an indicator of cell metabolic activity.Results are graphed as luminescent values (FIG. 1).

We can conclude that the covalent nature of the compounds E9 and E17allow for a long term effect in cells, even after compound is removed.Conversely, dinaciclib has a strong effect on cell viability when it ismaintained in culture, however, once it is removed, cells are able toreinitiate growth. Taken together, this indicates that the covalentnature of E9 and E17 has the advantage of short dosing periodstranslating into longer term effects.

Washout Expression Assay

Jurkat cells were treated with 1 uM of compound E9, E17, Dinaciclib orDMSO control (FIG. 3). 4 hours after treatment, cells were either nottreated or washed three times with RPMI media to remove all compound.Cells were replated and allowed to grow for 6 hours. Cells wereharvested, washed 3 times with PBS and resuspended in RIPA buffer (25 mMTris-HCl (pH 7.6), 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1%SDS). Equal amount of protein was loaded onto gel and blotted for Pol IISer2 (Millipore 04-1571), total pol II (Santa Cruz 17798), Tubulin (CellSignaling 11H10) or MCL1 (Cell Signaling 4572S)

We can see that when we treat with any of the compounds that Ser2phosphorylation and MCL1 levels are decreased. However, when we washoutthe compounds, only our covalent compounds are able to have an effectafter the washout whereas dinaciclib is unable to continue this effect.

TABLE A1 Biological evaluation of the exemplified compounds (IC50values/nM) Compound Structure CDK7/CycH CDK9/CycT Jurkat CDK2/CycASB1-E-24

    774  140 —    1260 SB1-E-19

    383  123 —     295 THZ-4-124-1

    122  373 117     976 SB1-E-22

    246   88.9 —   28300 SB1-E-25

    410  387 —   33400 THZ-5-38-1

     25.9  220 —     563 THZ-3-49-1

      9.43  445 4029 — THZ-4-119-1

     11.5  519 1960 — THZ-4-128-1

     46.8   73.4 1037   17100 THZ-4-141-1

   3600 3570 —  >1000 THZ-4-148-1

>10000 1710 —    7050 THZ-4-149-1

   4430 2290 —  >1000 X1

— — — — X2

— — — — X3

— — — — X4

— — — —

TABLE A2 Biological evaluation of additional exemplified compounds (IC50values/nM) Compound Structure CDK7/CycH CDK9/CycT Jurkat CDK2/CycATHZ-4-134-1

1180 379 522     163 THZ-5-18-1

121 1530 1336 — E-9(SB1-E-23)

1090 21.6 78.8     250 THZ-5-18-1

121 1530 1336 — E-1(SB1-E-14)

254 1360 —     735 SB1-E-18

461 41.8 19.2      15.0 SB1-E-21

1210 226 318    1220 SB1-E-26

1090 429 518     939 SB1-E-15 763 58.9 —    1480 SB1-E-16 255 116 —     30.3 SB1-E-17 1020 171 60.6     247 Y1

— — — — Y2

— — — — Y3

— — — — Y4

— — — — Y5

— — — — Y6

— — — — Y7

— — — — Y8

— — — — Y9

— — — — Y10

— — — — Y11

— — — — Y12

— — — — Y13

— — — — Y14

— — — — MFH-1-169-1

7250 135 —    3880 MFH-1-175-1

442 48.2 —    1080 MFH-1-187-1

279 23.5 —     171 MFH-2-67-1

23.7 103 —    1020 MFH-2-78-1

842 68.7 —  >1000 MFH-1-49-1

165 2.8 —      27.6 MFH-1-56-1

345 300    1530 MFH-1-143-1

2510 859 >10000 MFH-1-167-1

739 24.7     328 MFH-2-53-1

1100 61.6      53.5 MFH-3-140-1

356 465    4190 MFH-1-141-1

1210 23.9     932

Example 31. KiNativ™ Kinome Profiling

Jurkat cells were seeded at a density of 100 million cells/50 mL. Cellswere treated with E9 (1 μM) or DMSO control for 6 hrs. Cells were washedtwice with cold phosphate-buffered saline (PBS). PBS-washed cell pelletswere flash frozen and subjected to KiNativ™ kinome profiling at ActivXBiosciences, Inc. according to their specifications using theirdesthiobiotin-ATP probe. Peptide sequences shown in Table A4 belong tothe indicated kinase(s) and were detected by mass spectrometry (MS)under DMSO control conditions following enrichment for biotinylatedproteins by streptavidin pulldown and subsequent proteolysis. Kinaseslabeled by the reactive desthiobiotin-ATP probe indicate that the kinasewas accessible to desthiobiotin-ATP probe binding. Results shown arenormalized to these paired DMSO controls and numbers represent thepercentage (compared to DMSO control) of MS signal lost for sequences ofan indicated kinase, eg—numbers approaching 100% indicate that testcompound effectively out-competed the desthiobiotin ATP probe forbinding to the kinase, resulting in decreased labeling and enrichmentfor peptides representing this kinase. This result suggests that E9binds predominantly CDK12 and CDK13 in Jurkat cells (FIG. 10)

Example 32. Jurkat Gene Expression Analysis

Jurkat cells were seeded at a density of 5 million cells/10 mL. Cellswere then treated with 200 nM or 1 μM of the indicated compounds or withDMSO control for 6 hrs. Total RNA was extracted from 5 million cellsusing the RNeasy Plus Mini Kit (Qiagen) with a gDNA eliminator minicolumn to remove genomic DNA. mRNA was reverse transcribed into cDNAusing the SuperScript III First-Strand Synthesis Kit (Life Technologies)using an oligo-dT primer to capture polyadenylated mRNAs. QuantitativePCR (qPCR) using transcript-specific Taqman probes (Applied Biosystems)was used to assess the effect of compound treatment on the expression ofthe indicated mRNA transcripts. All experiments shown were performed inbiological triplicate. Each individual biological sample wasqPCR-amplified in technical duplicate. Error bars are +/−SD. Expressiondata from drug treatments were normalized to GAPDH probe.

These results suggest that the covalent inhibitors E9, E17, and E18 aswell as Dinaciclib (FIG. 6), a reversible inhibitor, potentlydownregulate the key T-ALL transcription factors TAL1, RUNX1, and MYB ata dose of 200 nM. Inhibitors E21 and E26 downregulate these factors to alesser degree at 200 nM and only potently reduce these transcripts at 1μM. Furthermore, the magnitude with which these inhibitors downregulatethe expression of these transcription factors at 200 nM correlates withtheir effective IC50s on Jurkat T-ALL cell proliferation. For example,Dinaciclib and E18 downregulate these transcription factor genes by atleast 80% at 200 nM and have IC50s less than 20 nM. E9 and E17downregulate these transcription factor genes by at least 40% at 200 nMand have IC50s less than 100 nM. Lastly, E21 and E26 downregulate thesegenes between 0-60% and have IC50s greater than 300 nM. This suggeststhat the magnitude of the reduction in expression of these transcriptionfactor genes may serve as an indicator of overall phenotypic response tothe inhibitor.

Example 33. Mutagenesis Analysis

Genome Editing:

The CRISPR/Cas9 system was used to mutate the endogenous CDK12 and CDK13loci to encode for CDK12 C1039S and CDK13 C1017S, both of which areputative CDK12/13 inhibitor-refractory mutants. Target-specificoligonucleotides were cloned into pX330, which carries a codon-optimizedversion of Cas9 and was further modified to express GFP for identifyingtransfectants. Cells were co-transfected (X-tremeGENE 9 (Roche)) with 1)pX330 expressing Cas9 and CDK12-targeting guide RNAs and 2) a pUC57-AMPconstruct bearing 1500 bp of modified CDK12 reference genome* that iscentered around the CRISPR targeting site in CDK12. Two days aftertransfection, cells were sorted using GFP as a marker of transfectedcells and cells were re-plated for five days. Cells were then re-platedat low density to facilitate the isolation of individual clones.Individual clones were isolated, expanded, and PCR genotyped usingmutant specific PCR primers. Following initial PCR screening, individualclones were Sanger sequenced to confirm the presence of the desiredmutation. Western blot confirmed the presence of intact CDK12 kinase.The process was sequentially repeated with Cas9/sgRNA constructs totarget and replace the CDK13 genetic loci. Subsequent experiments wereconducted using a CDK12 C1039S/CDK13 C1017S clone and a wild typecontrol clone that was carried through the entirety of the CRISPRprotocol but that was verified by Sanger sequencing to be wild typeT forCDK12 and CDK13. The genomic sequence complementary to theCDK12-directed guide RNA that was cloned into pX330 and used in thegenome editing experiments is: GGCAGGATTGCCATGAGTTG. The genomicsequence complementary to the CDK13-directed guide RNA that was clonedinto pX330 and used in the genome editing experiments is:GGCAAGATTGTCATGAGTTA. * The reference genome sequence used as a repairtemplate for CDK12 and CDK13 CRISPR was edited to 1) introduce DNAcoding for serine, 2) introduce mutations to either remove the PAM site(NGG) targeted by CRISPR/Cas9 or introduce sufficient wobble mutationssuch that the guide RNA could not recognize the repair template and thuscould not be cut by CRISPR/Cas9, and 3) introduce mutations that couldallow for mutant and wild type-specific PCR amplification.

HAP1 Cell Proliferation Assay:

HAP1 wild type and double mutants cells were seeded at a density of12,000 cells/well in 96-well plates. Twenty four hours cells were thentreated with the indicated compounds in a 10-pt dose escalation formatfrom 1 nM to 10 μM or DMSO control for 72 hrs. After 72 hrs, cells wereassayed using CellTiter-Glo Luminescent Cell Viability Assay (Promega)to determine cell viability by measuring the amount of ATP present ineach sample cell population, which is an indicator of cell metabolicactivity. Results are graphed as fraction of the DMSO control at 72 hrs.All data points were performed in biological triplicate. Error bars are+/−SD.

HAP1 cells expressing inhibitor-refractory mutations in CDK12 (C1039S)and CDK13 (C1017S) were 4-fold less sensitive to E17 compared to controlwild type HAP1 cells. This result indicates that a significant portionof intracellular E17 activity comes from covalent inhibition of CDK12and/or CDK13. Mutation of these targeted cysteines to a lessnucleophilic serine is sufficient to rescue a significant portion ofanti-proliferative activity at concentrations less than 350 nM.

EQUIVALENTS AND SCOPE

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process.

Furthermore, the invention encompasses all variations, combinations, andpermutations in which one or more limitations, elements, clauses, anddescriptive terms from one or more of the listed claims is introducedinto another claim. For example, any claim that is dependent on anotherclaim can be modified to include one or more limitations found in anyother claim that is dependent on the same base claim. Where elements arepresented as lists, e.g., in Markush group format, each subgroup of theelements is also disclosed, and any element(s) can be removed from thegroup. It should it be understood that, in general, where the invention,or aspects of the invention, is/are referred to as comprising particularelements and/or features, certain embodiments of the invention oraspects of the invention consist, or consist essentially of, suchelements and/or features. For purposes of simplicity, those embodimentshave not been specifically set forth in haec verba herein. It is alsonoted that the terms “comprising” and “containing” are intended to beopen and permits the inclusion of additional elements or steps. Whereranges are given, endpoints are included. Furthermore, unless otherwiseindicated or otherwise evident from the context and understanding of oneof ordinary skill in the art, values that are expressed as ranges canassume any specific value or sub-range within the stated ranges indifferent embodiments of the invention, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,but rather is as set forth in the appended claims. Those of ordinaryskill in the art will appreciate that various changes and modificationsto this description may be made without departing from the spirit orscope of the present invention, as defined in the following claims.

What is claimed is:
 1. A compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein: R¹ is optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted aryl, optionally substituted heterocyclyl, optionallysubstituted heteroaryl, —NR^(a)R^(b), —SR^(b), —C(═O)R^(b),—C(═O)OR^(b), or —C(═O)NR^(a)R^(b), wherein each instance of R^(a) andR^(b) is independently hydrogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted aryl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, a nitrogen protecting group whenattached to nitrogen, an oxygen protecting group when attached tooxygen, or a sulfur protecting group when attached to sulfur; or R^(a)and R^(b) are joined to form an optionally substituted heterocyclic oroptionally substituted heteroaryl ring; R³ is hydrogen, halogen, oroptionally substituted C₁-C₆ alkyl; R⁴ is halogen or optionallysubstituted C₁-C₆ alkyl; L¹ is a bond, —NR^(L1)—(CH₂)_(t)—, —O—, or —S—;R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group; t is 0 or an integer between 1 and 5, inclusive; RingA is optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl; L² is a bond, optionally substituted C₁₋₄ alkylene, —C(═O)—,—NR^(L2)—, —C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2)is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group; Ring B is absent, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl; and R² is any one of the formulae:

wherein: L³ is a bond or an optionally substituted C₁₋₄ hydrocarbonchain, optionally wherein one or more carbon units of the hydrocarbonchain are independently replaced with —C═O—, —O—, —S—, —NR^(L3a)—,—NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein each occurrence ofR^(L3a) is independently hydrogen, substituted or unsubstituted C₁₋₆alkyl, or a nitrogen protecting group, and wherein each occurrence ofR^(L3b) is independently hydrogen, halogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, or optionally substituted heteroaryl, ortwo R^(L3b) groups are joined to form an optionally substitutedcarbocyclic or optionally substituted heterocyclic ring; L⁴ is a bond oran optionally substituted, branched or unbranched C₁₋₆ hydrocarbonchain; each of R^(E1), R^(E2), and R^(E3) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, —CN, —CH₂OR^(EE), —CH₂N(R^(EE))₂,—CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, or —SR^(EE), whereineach occurrence of R^(EE) is independently hydrogen, optionallysubstituted alkyl, optionally substituted alkoxy, optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, or optionally substituted heteroaryl, or two R^(EE) groups arejoined to form an optionally substituted heterocyclic ring; or R^(E1)and R^(E3), or R^(E2) and R^(E3), or R^(E1) and R^(E2) are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring; R^(E4) is a leaving group; R^(E5) is halogen; R^(E6)is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group; each instance of Y is independently O, S, or NR^(E7),wherein R^(E7) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, ora nitrogen protecting group; a is 1 or 2; and each instance of z isindependently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
 2. Apharmaceutical composition comprising a compound of claim 1, or apharmaceutically acceptable salt thereof, and a pharmaceuticallyacceptable excipient.
 3. A kit comprising: a compound of claim 1, or apharmaceutically acceptable salt thereof; and instructions foradministering to a subject or contacting a biological sample with thecompound, or a pharmaceutically acceptable salt thereof.
 4. The compoundof claim 1, or a pharmaceutically acceptable salt thereof, wherein RingA comprises an optionally substituted phenyl ring.
 5. The compound ofclaim 1, or a pharmaceutically acceptable salt thereof, wherein Ring Acomprises an optionally substituted cyclohexyl ring.
 6. The compound ofclaim 1, or a pharmaceutically acceptable salt thereof, wherein L¹ is—NR^(L1)—.
 7. The compound of claim 1, or a pharmaceutically acceptablesalt thereof, wherein L² is —NR^(L2)(C═O)—.
 8. The compound of claim 1,or a pharmaceutically acceptable salt thereof, wherein Ring B is absent.9. The compound of claim 1, or a pharmaceutically acceptable saltthereof, wherein Ring B is an optionally substituted phenyl ring. 10.The compound of claim 1, or a pharmaceutically acceptable salt thereof,wherein R¹ is of Formula (n-1):

wherein: each instance of R^(1a) is independently hydrogen, halogen,optionally substituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1); eachinstance of R^(N1) is independently hydrogen, optionally substitutedC₁-C₆ alkyl, or a nitrogen protecting group; each instance of R^(O1) isindependently hydrogen, optionally substituted C₁-C₆ alkyl, or an oxygenprotecting group; and a1 is 0 or an integer between 1 and 6, inclusive.11. The compound of claim 1, or a pharmaceutically acceptable saltthereof, wherein R¹ is of Formula (n-2):

wherein: each instance of R^(1b) is independently hydrogen, halogen,optionally substituted C₁-C₆ alkyl, —N(R^(N1))₂, or —OR^(O1); eachinstance of R^(N1) is independently hydrogen, optionally substitutedC₁-C₆ alkyl, or a nitrogen protecting group; each instance of R^(O1) isindependently hydrogen, optionally substituted C₁-C₆ alkyl, or an oxygenprotecting group; and b1 is 0 or an integer between 1 and 6, inclusive.12. The compound of claim 1, wherein the compound is of Formula (II-1):

or a pharmaceutically acceptable salt thereof, wherein: each instance ofR^(1a) is independently hydrogen, halogen, optionally substituted C₁-C₆alkyl, —N(R^(N1))₂, or —OR^(O1); each instance of R^(N1) isindependently hydrogen, optionally substituted C₁-C₆ alkyl, or anitrogen protecting group; each instance of R^(O1) is independentlyhydrogen, optionally substituted C₁-C₆ alkyl, or an oxygen protectinggroup; and a1 is 0 or an integer between 1 and 6, inclusive.
 13. Thecompound of claim 12, wherein the compound is of Formula (II-1-a):

or a pharmaceutically acceptable salt thereof.
 14. The compound of claim12, wherein the compound is of Formula (II-1-a-i):

or a pharmaceutically acceptable salt thereof.
 15. The compound of claim12, wherein the compound is of Formula:

or a pharmaceutically acceptable salt thereof.
 16. The compound of claim1, wherein the compound is of Formula (II-2):

or a pharmaceutically acceptable salt thereof, wherein: each instance ofR^(1b) is independently hydrogen, halogen, optionally substituted C₁-C₆alkyl, —N(R^(N1))₂, or —OR^(O1); each instance of R^(N1) isindependently hydrogen, optionally substituted C₁-C₆ alkyl, or anitrogen protecting group; each instance of R^(O1) is independentlyhydrogen, optionally substituted C₁-C₆ alkyl, or an oxygen protectinggroup; and b1 is 0 or an integer between 1 and 6, inclusive.
 17. Thecompound of claim 1, or a pharmaceutically acceptable salt thereof,wherein R² is of Formula (i-1):


18. The compound of claim 1, or a pharmaceutically acceptable saltthereof, wherein R² is:


19. The compound of claim 1, wherein the compound is of the Formula:

or a pharmaceutically acceptable salt thereof.
 20. The compound of claim1, or a pharmaceutically acceptable salt thereof, wherein R¹ is—NR^(a)R^(b).
 21. The compound of claim 1, or a pharmaceuticallyacceptable salt thereof, wherein Ring A is an optionally substitutedphenyl ring.
 22. The compound of claim 1, or a pharmaceuticallyacceptable salt thereof, wherein Ring A is an optionally substitutedcyclohexyl ring.
 23. The compound of claim 1, or a pharmaceuticallyacceptable salt thereof, wherein Ring B is absent, and L² is a bond. 24.The compound of claim 17, or a pharmaceutically acceptable salt thereof,wherein Y is O.